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19 pages, 3666 KiB

Open AccessArticle

Genetic Diversity and Population Structure of Maize (Zea mays L.) Inbred Lines in Association with Phenotypic and Grain Qualitative Traits Using SSR Genotyping

by Rumit Patel, Juned Memon, Sushil Kumar, Dipak A. Patel, Amar A. Sakure, Manish B. Patel, Arna Das, Chikkappa G. Karjagi, Swati Patel, Ujjaval Patel and Rajib Roychowdhury

Plants 2024, 13(6), 823; https://doi.org/10.3390/plants13060823 - 13 Mar 2024

Cited by 4 | Viewed by 2034

Abstract

Maize (Zea mays L.) is an important cereal and is affected by climate change. Therefore, the production of climate-smart maize is urgently needed by preserving diverse genetic backgrounds through the exploration of their genetic diversity. To achieve this, 96 maize inbred lines [...] Read more.

Maize (Zea mays L.) is an important cereal and is affected by climate change. Therefore, the production of climate-smart maize is urgently needed by preserving diverse genetic backgrounds through the exploration of their genetic diversity. To achieve this, 96 maize inbred lines were used to screen for phenotypic yield-associated traits and grain quality parameters. These traits were studied across two different environments (Anand and Godhra) and polymorphic simple sequence repeat (SSR) markers were employed to investigate the genetic diversity, population structure, and trait-linked association. Genotype–environment interaction (GEI) reveals that most of the phenotypic traits were governed by the genotype itself across the environments, except for plant and ear height, which largely interact with the environment. The genotypic correlation was found to be positive and significant among protein, lysine and tryptophan content. Similarly, yield-attributing traits like ear girth, kernel rows ear⁻¹, kernels row⁻¹ and number of kernels ear⁻¹ were strongly correlated to each other. Pair-wise genetic distance ranged from 0.0983 (1820194/T1 and 1820192/4-20) to 0.7377 (IGI-1101 and 1820168/T1). The SSRs can discriminate the maize population into three distinct groups and shortlisted two genotypes (IGI-1101 and 1820168/T1) as highly diverse lines. Out of the studied 136 SSRs, 61 were polymorphic to amplify a total of 131 alleles (2–3 per loci) with 0.46 average gene diversity. The Polymorphism Information Content (PIC) ranged from 0.24 (umc1578) to 0.58 (umc2252). Similarly, population structure analysis revealed three distinct groups with 19.79% admixture among the genotypes. Genome-wide scanning through a mixed linear model identifies the stable association of the markers umc2038, umc2050 and umc2296 with protein, umc2296 and umc2252 with tryptophan, and umc1535 and umc1303 with total soluble sugar. The obtained maize lines and SSRs can be utilized in future maize breeding programs in relation to other trait characterizations, developments, and subsequent molecular breeding performances for trait introgression into elite genotypes. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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24 pages, 3856 KiB

Open AccessArticle

Rice (Oryza sativa L.) Grain Size, Shape, and Weight-Related QTLs Identified Using GWAS with Multiple GAPIT Models and High-Density SNP Chip DNA Markers

by Nkulu Rolly Kabange, Gamenyah Daniel Dzorkpe, Dong-Soo Park, Youngho Kwon, Sais-Beul Lee, So-Myeong Lee, Ju-Won Kang, Seong-Gyu Jang, Ki-Won Oh and Jong-Hee Lee

Plants 2023, 12(23), 4044; https://doi.org/10.3390/plants12234044 - 30 Nov 2023

Cited by 2 | Viewed by 1689

Abstract

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway [...] Read more.

This study investigated novel quantitative traits loci (QTLs) associated with the control of grain shape and size as well as grain weight in rice. We employed a joint-strategy multiple GAPIT (Genome Association and Prediction Integrated Tool) models [(Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK)), Fixed and random model Circulating Probability Uniform (FarmCPU), Settlement of MLM Under Progressive Exclusive Relationship (SUPER), and General Linear Model (GLM)]–High-Density SNP Chip DNA Markers (60,461) to conduct a Genome-Wide Association Study (GWAS). GWAS was performed using genotype and grain-related phenotypes of 143 recombinant inbred lines (RILs). Data show that parental lines (Ilpum and Tung Tin Wan Hein 1, TTWH1, Oryza sativa L., ssp. japonica and indica, respectively) exhibited divergent phenotypes for all analyzed grain traits), which was reflected in their derived population. GWAS results revealed the association between seven SNP Chip makers and QTLs for grain length, co-detected by all GAPIT models on chromosomes (Chr) 1–3, 5, 7, and 11, were qGL1-1^BFSG (AX-95918134, Chr1: 3,820,526 bp) explains 65.2–72.5% of the phenotypic variance explained (PVE). In addition, qGW1-1^BFSG (AX-273945773, Chr1: 5,623,288 bp) for grain width explains 15.5–18.9% of PVE. Furthermore, BLINK or FarmCPU identified three QTLs for grain thickness independently, and explain 74.9% (qGT1^Blink, AX-279261704, Chr1: 18,023,142 bp) and 54.9% (qGT2-1^Farm, AX-154787777, Chr2: 2,118,477 bp) of the observed PVE. For the grain length-to-width ratio (LWR), the qLWR2^BFSG (AX-274833045, Chr2: 10,000,097 bp) explains nearly 15.2–32% of the observed PVE. Likewise, the major QTL for thousand-grain weight (TGW) was detected on Chr6 (qTGW6^BFSG, AX-115737727, 28,484,619 bp) and explains 32.8–54% of PVE. The qTGW6^BFSG QTL coincides with qGW6-1^Blink for grain width and explained 32.8–54% of PVE. Putative candidate genes pooled from major QTLs for each grain trait have interesting annotated functions that require functional studies to elucidate their function in the control of grain size, shape, or weight in rice. Genome selection analysis proposed makers useful for downstream marker-assisted selection based on genetic merit of RILs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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10 pages, 304 KiB

Open AccessArticle

Combining Ability and Reciprocal Effects for the Yield of Elite Blue Corn Lines from the Central Highlands of Mexico

by José Luis Arellano-Vázquez, Germán Fernando Gutiérrez-Hernández, Luis Fernando Ceja-Torres, Estela Flores-Gómez, Elpidio García-Ramírez, Francisco Roberto Quiroz-Figueroa and Patricia Vázquez-Lozano

Plants 2023, 12(22), 3861; https://doi.org/10.3390/plants12223861 - 15 Nov 2023

Cited by 1 | Viewed by 1015

Abstract

The development of hybrid plants can increase the production and quality of blue corn, and, thus, satisfy its high demand. For this development, it is essential to understand the heterotic relationships of the germplasm. The objectives of this study were to determine the [...] Read more.

The development of hybrid plants can increase the production and quality of blue corn, and, thus, satisfy its high demand. For this development, it is essential to understand the heterotic relationships of the germplasm. The objectives of this study were to determine the effects of general (GCA) and specific (SCA) combining ability, as well as the reciprocal effects (REs) on the yields of 10 blue corn lines, and to select the outstanding lines. Diallel crosses were generated with 10 lines and evaluated at the Valle de México Experimental Station in Chapingo, Mexico, and Calpulalpan, Tlaxcala, Mexico. There were differences (p ≤ 0.01) in the hybrids, Loc, effects of GCA, SCA, and REs, and in the following interactions: hybrids × Loc, GCA × Loc, SCA × Loc, and RE × Loc. For GCA, lines Ll, L4, L6, and L9 stood out, with significant values of 3.4, 2.9, 2.9, and 3.1, respectively. For SCA, the hybrids featured were L4 × L10, L2 × L10, L1 × L10, L7 × L8, and L2 × L6, with values of 3.0, 2.5, 2.3, 2.3, and 2.2, and yields of 11.2, 10.2, 10.4, 10.4, and 10.5 t ha^−l, respectively. There were no significant REs in these lines. Considerable effects of GCA and SCA were detected; therefore, we concluded that native populations had favorable dominance and additive genetic effects that could be used to support the development of high-yielding lines and hybrids. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

21 pages, 5183 KiB

Open AccessArticle

Evaluation of Morpho-Physiological and Yield-Associated Traits of Rice (Oryza sativa L.) Landraces Combined with Marker-Assisted Selection under High-Temperature Stress and Elevated Atmospheric CO₂ Levels

by Merentoshi Mollier, Rajib Roychowdhury, Lanunola Tzudir, Radheshyam Sharma, Ujjal Barua, Naseema Rahman, Sikandar Pal, Bhabesh Gogoi, Prakash Kalita, Devendra Jain and Ranjan Das

Plants 2023, 12(20), 3655; https://doi.org/10.3390/plants12203655 - 23 Oct 2023

Cited by 1 | Viewed by 1913

Abstract

Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI [...] Read more.

Rice (Oryza sativa L.) is an important cereal crop worldwide due to its long domestication history. North-Eastern India (NEI) is one of the origins of indica rice and contains various native landraces that can withstand climatic changes. The present study compared NEI rice landraces to a check variety for phenological, morpho-physiological, and yield-associated traits under high temperatures (HTs) and elevated CO₂ (eCO₂) levels using molecular markers. The first experiment tested 75 rice landraces for HT tolerance. Seven better-performing landraces and the check variety (N22) were evaluated for the above traits in bioreactors for two years (2019 and 2020) under control (T1) and two stress treatments [mild stress or T2 (eCO₂ 550 ppm + 4 °C more than ambient temperature) and severe stress or T3 (eCO₂ 750 ppm + 6 °C more than ambient temperature)]. The findings showed that moderate stress (T2) improved plant height (PH), leaf number (LN), leaf area (LA), spikelets panicle⁻¹ (S/P), thousand-grain weight (TGW), harvest index (HI), and grain production. HT and eCO₂ in T3 significantly decreased all genotypes’ metrics, including grain yield (GY). Pollen traits are strongly and positively associated with spikelet fertility at maturity and GY under stress conditions. Shoot biomass positively affected yield-associated traits including S/P, TGW, HI, and GY. This study recorded an average reduction of 8.09% GY across two seasons in response to the conditions simulated in T3. Overall, two landraces—Kohima special and Lisem—were found to be more responsive compared to other the landraces as well as N22 under stress conditions, with a higher yield and biomass increment. SCoT-marker-assisted genotyping amplified 77 alleles, 55 of which were polymorphic, with polymorphism information content (PIC) values from 0.22 to 0.67. The study reveals genetic variation among the rice lines and supports Kohima Special and Lisem’s close relationship. These two better-performing rice landraces are useful pre-breeding resources for future rice-breeding programs to increase stress tolerance, especially to HT and high eCO₂ levels under changing climatic situations. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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23 pages, 3360 KiB

Open AccessArticle

Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum

by Barbara Pipan, Lovro Sinkovič, Mohamed Neji, Dagmar Janovská, Meiliang Zhou and Vladimir Meglič

Plants 2023, 12(18), 3321; https://doi.org/10.3390/plants12183321 - 20 Sep 2023

Cited by 1 | Viewed by 1544

Abstract

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species [...] Read more.

Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei’s expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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15 pages, 2534 KiB

Open AccessArticle

Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice

by Xu Jiang, Woo-Jong Hong, Su-Kyoung Lee and Ki-Hong Jung

Plants 2023, 12(16), 2959; https://doi.org/10.3390/plants12162959 - 16 Aug 2023

Viewed by 1668

Abstract

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop [...] Read more.

The collar region plays a crucial role in leaf angle formation and plant architecture, which is important for improving crop yield given the challenges of diminishing arable land and changing environmental conditions. To determine collar region-preferential genes (CRPGs) affecting plant architecture and crop yield, we conducted genome-wide transcriptomic analysis. By integrating our RNA sequencing data with public rice anatomical expression data, we identified 657 CRPGs. Verification involved testing six randomly selected CRPGs, all of which exhibited collar-preferential expression. The functional significance of CRPGs was assessed via Gene Ontology enrichment analysis, utilizing MapMan and KEGG, and literature analysis provided additional information for characterized CRPGs. Our findings revealed links between manipulating leaf angle and phytohormone-related pathways and stress responses. Moreover, based on the CRPGs, five transcription factors downstream of the liguleless 1 (LG1) gene were identified. Overall, the identified CRPGs provide potential targets for further research and breeding applications aimed at improving crop productivity by manipulating leaf architecture. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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19 pages, 3197 KiB

Open AccessArticle

Construction of High-Density Genetic Map and QTL Mapping for Grain Shape in the Rice RIL Population

by Minyi Wei, Tongping Luo, Dahui Huang, Zengfeng Ma, Chi Liu, Yuanyuan Qin, Zishuai Wu, Xiaolong Zhou, Yingping Lu, Liuhui Yan, Gang Qin and Yuexiong Zhang

Plants 2023, 12(16), 2911; https://doi.org/10.3390/plants12162911 - 10 Aug 2023

Cited by 1 | Viewed by 1213

Abstract

Grain shape is an important agronomic trait directly associated with yield in rice. In order to explore new genes related to rice grain shape, a high-density genetic map containing 2193 Bin markers (526957 SNP) was constructed by whole-genome resequencing of 208 recombinant inbred [...] Read more.

Grain shape is an important agronomic trait directly associated with yield in rice. In order to explore new genes related to rice grain shape, a high-density genetic map containing 2193 Bin markers (526957 SNP) was constructed by whole-genome resequencing of 208 recombinant inbred (RILs) derived from a cross between ZP37 and R8605, with a total genetic distance of 1542.27 cM. The average genetic distance between markers was 0.76 cM, and the physical distance was 201.29 kb. Quantitative trait locus (QTL) mapping was performed for six agronomic traits related to rice grain length, grain width, length-to-width ratio, thousand-grain weight, grain cross-sectional area, and grain perimeter under three different environments. A total of 39 QTLs were identified, with mapping intervals ranging from 8.1 kb to 1781.6 kb and an average physical distance of 517.5 kb. Among them, 15 QTLs were repeatedly detected in multiple environments. Analysis of the genetic effects of the identified QTLs revealed 14 stable genetic loci, including three loci that overlapped with previously reported gene positions, and the remaining 11 loci were newly identified loci associated with two or more environments or traits. Locus 1, Locus 3, Locus 10, and Locus 14 were novel loci exhibiting pleiotropic effects on at least three traits and were detected in multiple environments. Locus 14, with a contribution rate greater than 10%, influenced grain width, length-to-width ratio, and grain cross-sectional area. Furthermore, pyramiding effects analysis of three stable genetic loci showed that increasing the number of QTL could effectively improve the phenotypic value of grain shape. Collectively, our findings provided a theoretical basis and genetic resources for the cloning, functional analysis, and molecular breeding of genes related to rice grain shape. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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23 pages, 5545 KiB

Open AccessArticle

Genome-Wide Association Study Identified Candidate Genes for Alkalinity Tolerance in Rice

by Lovepreet Singh, Rajat Pruthi, Sandeep Chapagain and Prasanta K. Subudhi

Plants 2023, 12(11), 2206; https://doi.org/10.3390/plants12112206 - 3 Jun 2023

Cited by 1 | Viewed by 1908

Abstract

Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica [...] Read more.

Alkalinity stress is a major hindrance to enhancing rice production globally due to its damaging effect on plants’ growth and development compared with salinity stress. However, understanding of the physiological and molecular mechanisms of alkalinity tolerance is limited. Therefore, a panel of indica and japonica rice genotypes was evaluated for alkalinity tolerance at the seedling stage in a genome-wide association study to identify tolerant genotypes and candidate genes. Principal component analysis revealed that traits such as alkalinity tolerance score, shoot dry weight, and shoot fresh weight had the highest contribution to variations in tolerance, while shoot Na⁺ concentration, shoot Na⁺:K⁺ ratio, and root-to-shoot ratio had moderate contributions. Phenotypic clustering and population structure analysis grouped the genotypes into five subgroups. Several salt-susceptible genotypes such as IR29, Cocodrie, and Cheniere placed in the highly tolerant cluster suggesting different underlying tolerance mechanisms for salinity and alkalinity tolerance. Twenty-nine significant SNPs associated with alkalinity tolerance were identified. In addition to three alkalinity tolerance QTLs, qSNK4, qSNC9, and qSKC10, which co-localized with the earlier reported QTLs, a novel QTL, qSNC7, was identified. Six candidate genes that were differentially expressed between tolerant and susceptible genotypes were selected: LOC_Os04g50090 (Helix-loop-helix DNA-binding protein), LOC_Os08g23440 (amino acid permease family protein), LOC_Os09g32972 (MYB protein), LOC_Os08g25480 (Cytochrome P450), LOC_Os08g25390 (Bifunctional homoserine dehydrogenase), and LOC_Os09g38340 (C2H2 zinc finger protein). The genomic and genetic resources such as tolerant genotypes and candidate genes would be valuable for investigating the alkalinity tolerance mechanisms and for marker-assisted pyramiding of the favorable alleles for improving alkalinity tolerance at the seedling stage in rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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19 pages, 6976 KiB

Open AccessArticle

Identification and Expression Analysis of the Isopentenyl Transferase (IPT) Gene Family under Lack of Nitrogen Stress in Oilseed (Brassica napus L.)

by Jingdong Chen, Heping Wan, Wenhui Zhu, Xigang Dai, Yi Yu and Changli Zeng

Plants 2023, 12(11), 2166; https://doi.org/10.3390/plants12112166 - 30 May 2023

Cited by 2 | Viewed by 1609

Abstract

BnIPT gene family members in Brassica napus and analyzing their expression under different exogenous hormones and abiotic stress treatments to provide a theoretical basis for clarifying their functions and molecular genetic mechanisms in nitrogen deficiency stress tolerance of B. napus. Using the [...] Read more.

BnIPT gene family members in Brassica napus and analyzing their expression under different exogenous hormones and abiotic stress treatments to provide a theoretical basis for clarifying their functions and molecular genetic mechanisms in nitrogen deficiency stress tolerance of B. napus. Using the Arabidopsis IPT protein as the seed sequence, combined with the IPT protein domain PF01715, 26 members of the BnIPT gene family were identified from the whole genome of the rape variety ZS11. Additionally, the physicochemical properties and structures, phylogenetic relationships, synteny relationships, protein–protein interaction network, and gene ontology enrichment were analyzed. Based on transcriptome data, the expression patterns of the BnIPT gene under different exogenous hormone and abiotic stress treatments were analyzed. We used the qPCR method to identify the relative expression level of BnIPT genes that may be related to the stress resistance of rapeseed in transcriptome analysis under normal nitrogen (N: 6 mmol·L⁻¹) and nitrogen deficiency (N: 0) conditions and analyzed its effect on rapeseed under nitrogen deficiency stress role in tolerance. In response to nitrogen deficiency signals, the BnIPT gene showed a trend of up-regulation in shoots and down-regulation in roots, indicating that it may affect the process of nitrogen transport and redistribution to enhance the stress resistance of rapeseed to respond to the nitrogen deficiency stress. This study provides a theoretical basis for clarifying the function and molecular genetic mechanism of the BnIPT gene family in nitrogen deficiency stress tolerance in rape. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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28 pages, 2901 KiB

Open AccessArticle

Integrating BLUP, AMMI, and GGE Models to Explore GE Interactions for Adaptability and Stability of Winter Lentils (Lens culinaris Medik.)

by Md. Amir Hossain, Umakanta Sarker, Md. Golam Azam, Md. Shahriar Kobir, Rajib Roychowdhury, Sezai Ercisli, Daoud Ali, Shinya Oba and Kirill S. Golokhvast

Plants 2023, 12(11), 2079; https://doi.org/10.3390/plants12112079 - 23 May 2023

Cited by 21 | Viewed by 3192

Abstract

Lentil yield is a complicated quantitative trait; it is significantly influenced by the environment. It is crucial for improving human health and nutritional security in the country as well as for a sustainable agricultural system. The study was laid out to determine the [...] Read more.

Lentil yield is a complicated quantitative trait; it is significantly influenced by the environment. It is crucial for improving human health and nutritional security in the country as well as for a sustainable agricultural system. The study was laid out to determine the stable genotype through the collaboration of G × E by AMMI and GGE biplot and to identify the superior genotypes using 33 parametric and non-parametric stability statistics of 10 genotypes across four different conditions. The total G × E effect was divided into two primary components by the AMMI model. For days to flowering, days to maturity, plant height, pods per plant, and hundred seed weight, IPCA1 was significant and accounted for 83%, 75%, 100%, and 62%, respectively. Both IPCA1 and IPCA2 were non-significant for yield per plant and accounted for 62% of the overall G × E interaction. An estimated set of eight stability parameters showed strong positive correlations with mean seed yield, and these measurements can be utilized to choose stable genotypes. The productivity of lentils has varied greatly in the environment, ranging from 786 kg per ha in the MYM environment to 1658 kg per ha in the ISD environment, according to the AMMI biplot. Three genotypes (G8, G7, and G2) were shown to be the most stable based on non-parametric stability scores for grain yield. G8, G7, G2, and G5 were determined as the top lentil genotypes based on grain production using numerical stability metrics such as Francis’s coefficient of variation, Shukla stability value (σi²), and Wrick’s ecovalence (Wi). Genotypes G7, G10, and G4 were the most stable with the highest yield, according to BLUP-based simultaneous selection stability characteristics. The findings of graphic stability methods such as AMMI and GGE for identifying the high-yielding and stable lentil genotypes were very similar. While the GGE biplot indicated G2, G10, and G7 as the most stable and high-producing genotypes, AMMI analysis identified G2, G9, G10, and G7. These selected genotypes would be used to release a new variety. Considering all the stability models, such as Eberhart and Russell’s regression and deviation from regression, additive main effects, multiplicative interactions (AMMI) analysis, and GGE, the genotypes G2, G9, and G7 could be used as well-adapted genotypes with moderate grain yield in all tested environments. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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28 pages, 5312 KiB

Open AccessArticle

Genetic Analyses of Mungbean [Vigna radiata (L.) Wilczek] Breeding Traits for Selecting Superior Genotype(s) Using Multivariate and Multi-Traits Indexing Approaches

by Mohammad Golam Azam, Mohammad Amir Hossain, Umakanta Sarker, A. K. M. Mahabubul Alam, Ramakrishnan M. Nair, Rajib Roychowdhury, Sezai Ercisli and Kirill S. Golokhvast

Plants 2023, 12(10), 1984; https://doi.org/10.3390/plants12101984 - 15 May 2023

Cited by 19 | Viewed by 3759

Abstract

Mungbean [Vigna radiata (L.) Wilczek] is an important food, feed, and cash crop in rice-based agricultural ecosystems in Southeast Asia and other continents. It has the potential to enhance livelihoods due to its palatability, nutritional content, and digestibility. We evaluated 166 diverse [...] Read more.

Mungbean [Vigna radiata (L.) Wilczek] is an important food, feed, and cash crop in rice-based agricultural ecosystems in Southeast Asia and other continents. It has the potential to enhance livelihoods due to its palatability, nutritional content, and digestibility. We evaluated 166 diverse mungbean genotypes in two seasons using multivariate and multi-traits index approaches to identify superior genotypes. The total Shannon diversity index (SDI) for qualitative traits ranged from moderate for terminal leaflet shape (0.592) to high for seed colour (1.279). The analysis of variances (ANOVA) indicated a highly significant difference across the genotypes for most of the studied traits. Descriptive analyses showed high diversity among genotypes for all morphological traits. Six components with eigen values larger than one contributed 76.50% of the variability in the principal component analysis (PCA). The first three PCs accounted for the maximum 29.90%, 15.70%, and 11.20% of the total variances, respectively. Yield per plant, pod weight, hundred seed weight, pod length, days to maturity, pods per plant, harvest index, biological yield per plant, and pod per cluster contributed more to PC1 and PC2 and showed a positive association and positive direct effect on seed yield. The genotypes were grouped into seven clusters with the maximum in cluster II (34) and the minimum in cluster VII (10) along with a range of intra-cluster and inter-cluster distances of 5.15 (cluster II) to 3.60 (cluster VII) and 9.53 (between clusters II and VI) to 4.88 (clusters I and VII), suggesting extreme divergence and the possibility for use in hybridization and selection. Cluster III showed the highest yield and yield-related traits. Yield per plant positively and significantly correlated with pod traits and hundred seed weight. Depending on the multi-trait stability index (MTSI), clusters I, III, and VII might be utilized as parents in the hybridization program to generate high-yielding, disease-resistant, and small-seeded mungbean. Based on all multivariate-approaches, G45, G5, G22, G55, G143, G144, G87, G138, G110, G133, and G120 may be considered as the best parents for further breeding programs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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15 pages, 2841 KiB

Open AccessArticle

Marker-Assisted Improvement for Durable Bacterial Blight Resistance in Aromatic Rice Cultivar HUR 917 Popular in Eastern Parts of India

by Manish Kumar, Ravi Pratap Singh, Debarchana Jena, Vineeta Singh, Diptibala Rout, Panduranga Bhagwan Arsode, Madhu Choudhary, Prakash Singh, Suman Chahar, Sanghamitra Samantaray, Arup Kumar Mukherjee, Chander Mohan, Abhishek Bohra, Goutam Das, Sumana Balo, Onkar Nath Singh and Ramlakhan Verma

Plants 2023, 12(6), 1363; https://doi.org/10.3390/plants12061363 - 18 Mar 2023

Cited by 2 | Viewed by 2207

Abstract

Bacterial blight (BB) is a devastating disease of rice in the tropics of Indian sub-continent, where the presence of Xoo races with varying levels of genetic diversity and virulence renders disease management extremely challenging. In this context, marker-assisted improvement of plant resistance has [...] Read more.

Bacterial blight (BB) is a devastating disease of rice in the tropics of Indian sub-continent, where the presence of Xoo races with varying levels of genetic diversity and virulence renders disease management extremely challenging. In this context, marker-assisted improvement of plant resistance has been proven as one of the most promising approaches for the development of sustainable rice cultivars. The present study demonstrates the marker-assisted introgression of the three BB resistant genes (Xa21 + xa13 + xa5) into the background of HUR 917, a popular aromatic short grain (ASG) rice cultivar in India. The performance of the resulting improved products (near isogenic lines (NILs), HR 23-5-37-83-5, HR 23-5-37-121-10, HR 23-5-37-121-14, HR 23-65-6-191-13, HR 23-65-6-237-2, HR 23-65-6-258-10 and HR 23-65-6-258-21) establishes the utility of marker-assisted selection (MAS) approach for accelerated trait introgression in rice. The MAS-bred lines carrying three introgressed genes showed broad spectrum BB resistance (lesion length, LL of 1.06 ± 1.35 cm to 4.61 ± 0.87 cm). Besides, these improved lines showed the complete product profile of recurrent parent HUR 917 along with the enhanced level of durable BB resistance. The improved introgression lines with durable BB resistance would contribute to sustainable rice production in India, particularly in the Indo-Gangetic plane that has substantial acreage under HUR 917. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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17 pages, 1363 KiB

Open AccessArticle

Marker-Assisted Pyramiding of Blast-Resistance Genes in a japonica Elite Rice Cultivar through Forward and Background Selection

by Elisa Zampieri, Andrea Volante, Caterina Marè, Gabriele Orasen, Francesca Desiderio, Chiara Biselli, Marco Canella, Lorena Carmagnola, Joëlle Milazzo, Henri Adreit, Didier Tharreau, Nicolas Poncelet, Patrizia Vaccino and Giampiero Valè

Plants 2023, 12(4), 757; https://doi.org/10.3390/plants12040757 - 8 Feb 2023

Cited by 7 | Viewed by 2615

Abstract

Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of [...] Read more.

Rice blast, caused by Pyricularia oryzae, is one of the main rice diseases worldwide. The pyramiding of blast-resistance (Pi) genes, coupled to Marker-Assisted BackCrossing (MABC), provides broad-spectrum and potentially durable resistance while limiting the donor genome in the background of an elite cultivar. In this work, MABC coupled to foreground and background selections based on KASP marker assays has been applied to introgress four Pi genes (Piz, Pib, Pita, and Pik) in a renowned japonica Italian rice variety, highly susceptible to blast. Molecular analyses on the backcross (BC) lines highlighted the presence of an additional blast-resistance gene, the Pita-linked Pita2/Ptr gene, therefore increasing the number of blast-resistance introgressed genes to five. The recurrent genome was recovered up to 95.65%. Several lines carrying four (including Pita2) Pi genes with high recovery percentage levels were also obtained. Phenotypic evaluations confirmed the effectiveness of the pyramided lines against multivirulent strains, which also had broad patterns of resistance in comparison to those expected based on the pyramided Pi genes. The developed blast-resistant japonica lines represent useful donors of multiple blast-resistance genes for future rice-breeding programs related to the japonica group. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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14 pages, 1704 KiB

Open AccessArticle

Analysis of Domestication Loci in Wild Rice Populations

by Sharmin Hasan, Agnelo Furtado and Robert Henry

Plants 2023, 12(3), 489; https://doi.org/10.3390/plants12030489 - 20 Jan 2023

Cited by 1 | Viewed by 2162

Abstract

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation [...] Read more.

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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22 pages, 3858 KiB

Open AccessArticle

Novel Single-Nucleotide Variants for Morpho-Physiological Traits Involved in Enhancing Drought Stress Tolerance in Barley

by Ibrahim S. Elbasyoni, Shamseldeen Eltaher, Sabah Morsy, Alsayed M. Mashaheet, Ahmed M. Abdallah, Heba G. Ali, Samah A. Mariey, P. Stephen Baenziger and Katherine Frels

Plants 2022, 11(22), 3072; https://doi.org/10.3390/plants11223072 - 13 Nov 2022

Cited by 5 | Viewed by 1913

Abstract

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation [...] Read more.

Barley (Hordeum vulgare L.) thrives in the arid and semi-arid regions of the world; nevertheless, it suffers large grain yield losses due to drought stress. A panel of 426 lines of barley was evaluated in Egypt under deficit (DI) and full irrigation (FI) during the 2019 and 2020 growing seasons. Observations were recorded on the number of days to flowering (NDF), total chlorophyll content (CH), canopy temperature (CAN), grain filling duration (GFD), plant height (PH), and grain yield (Yield) under DI and FI. The lines were genotyped using the 9K Infinium iSelect single nucleotide polymorphisms (SNP) genotyping platform, which resulted in 6913 high-quality SNPs. In conjunction with the SNP markers, the phenotypic data were subjected to a genome-wide association scan (GWAS) using Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK). The GWAS results indicated that 36 SNPs were significantly associated with the studied traits under DI and FI. Furthermore, eight markers were significant and common across DI and FI water regimes, while 14 markers were uniquely associated with the studied traits under DI. Under DI and FI, three (11_10326, 11_20042, and 11_20170) and five (11_20099, 11_10326, 11_20840, 12_30298, and 11_20605) markers, respectively, had pleiotropic effect on at least two traits. Among the significant markers, 24 were annotated to known barley genes. Most of these genes were involved in plant responses to environmental stimuli such as drought. Overall, nine of the significant markers were previously reported, and 27 markers might be considered novel. Several markers identified in this study could enable the prediction of barley accessions with optimal agronomic performance under DI and FI. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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15 pages, 943 KiB

Open AccessArticle

Genetic Variability, Character Association, and Path Coefficient Analysis in Transplant Aman Rice Genotypes

by Abu Salah Muhammad Faysal, Liakat Ali, Md. Golam Azam, Umakanta Sarker, Sezai Ercisli, Kirill S. Golokhvast and Romina Alina Marc

Plants 2022, 11(21), 2952; https://doi.org/10.3390/plants11212952 - 2 Nov 2022

Cited by 32 | Viewed by 2762

Abstract

A field experiment was carried out with 20 genotypes of Transplant Aman (T. Aman) rice at the Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1706, Bangladesh. The study was performed to evaluate the genetic deviation, trait association, [...] Read more.

A field experiment was carried out with 20 genotypes of Transplant Aman (T. Aman) rice at the Department of Genetics and Plant Breeding, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Salna, Gazipur-1706, Bangladesh. The study was performed to evaluate the genetic deviation, trait association, and path coefficient (PC) based on grain yield (GY) and different yield-contributing agronomic characters. Variance analysis displayed extensive traits-wise variations across accessions, indicating variability and the opportunity for genetic selection for desirable traits. The high mean, range, and genotypic variances observed for most of the characters indicated a wide range of variation for these traits. All the characters indicated the minimum influence of environment on the expression of the trait and genetic factors had a significant role in the expressivity of these characters. High heritability in broad sense (h²_b) and high to moderate genetic advance in percent of the mean (GAPM) were recorded for all the characters except for panicle length (PL). Based on mean, range, and all genetic parameters, the selection of all the traits except for PL would contribute to the development of T. Aman rice genotypes. A correlation study revealed that selection based on plant height (PH), number of effective tillers per hill (NET), PL, number of filled spikelets per panicle (NFS), flag leaf length (FLL), spikelet sterility (SS) percentage, and harvest index (HI) would be effective for increasing the GY of rice. Genotypic correction with grain yield (GCGY), PC and principal component analysis (PCA) revealed that direct selection of NFS, HI, SS%, and FLL would be effective for improving the GY of rice in future breeding programs. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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26 pages, 8631 KiB

Open AccessArticle

Assessment of GGE, AMMI, Regression, and Its Deviation Model to Identify Stable Rice Hybrids in Bangladesh

by M Jamil Hasan, M Umma Kulsum, Umakanta Sarker, M Quamrul Islam Matin, Nazmul Hoque Shahin, M Shahjahan Kabir, Sezai Ercisli and Romina Alina Marc

Plants 2022, 11(18), 2336; https://doi.org/10.3390/plants11182336 - 7 Sep 2022

Cited by 25 | Viewed by 2123

Abstract

Twenty-six rice hybrids were evaluated at three locations. Data were normally distributed after running the Shapiro–Wilk test. Plant height and effective tillers/hills showed leptokurtic distribution, indicating these traits were controlled by fewer genes, whereas the rest of the attributes had platykurtic distribution, indicating [...] Read more.

Twenty-six rice hybrids were evaluated at three locations. Data were normally distributed after running the Shapiro–Wilk test. Plant height and effective tillers/hills showed leptokurtic distribution, indicating these traits were controlled by fewer genes, whereas the rest of the attributes had platykurtic distribution, indicating these traits were controlled by many genes. Most of the traits were significant for variety, locations, and variety × locations. For yield stability, the data were analyzed using additive main effect and multiplicative interaction (AMMI), genotype and genotype–environment interaction (GGE), and Eberhart and Russell’s model. Among 26 hybrids, BRRI99A × BRRI38R and BRRI hybrid dhan5 exhibited high yields at three locations. BRRI99A × BRRI45R, BRRI99A × BRRI31R, IR79156A × BRRI38R, and BRRI hybrid dhan3 were selected for mega-environments: Gazipur and Ishwardi. Among the tested locations, Gazipur (E2) and Ishwardi (E3) were identified as mega-environments for the hybrid combinations, including BRRI99A × BRRI36R, BRRI99A × BRRI49R, IR79156A × BRRI31R, IR79156A × BRRI38R, BRRI hybrid dhan5, BRRI99A × BRRI38R, BRRI99A × BRRI45R, and BRRI99A × BRRI31R based on their average action and fixity. Gazipur and Ishwardi were the best environments because their discriminative and representative ability was remarkable. The hybrid assessment, as well as area selection for hybrid rice breeding in Bangladesh, were revealed in this study. The hybrid BRRI99A × BRRI38R, BRRI99A × BRRI36R, and IR79156A × Rline7 belonged to medium-to-long slender grain types. Nowadays, the citizens of Bangladesh prefer fine-grain rice. Therefore, these fine-grain hybrids can be cultivated as preferable commercial varieties at three locations, such as Barisal, Gazipur, and Ishwardi in Bangladesh. The stable hybrids identified in the current study can be recommended for cultivation throughout the whole country without compromising the loss of grain yield of rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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13 pages, 871 KiB

Open AccessArticle

Genetic Analysis in Grain Legumes [Vigna radiata (L.) Wilczek] for Yield Improvement and Identifying Heterotic Hybrids

by Md. Golam Azam, Umakanta Sarker, Md. Amir Hossain, Md. Shahin Iqbal, Md. Rafiqul Islam, Md. Faruk Hossain, Sezai Ercisli, Raziye Kul, Amine Assouguem, Arwa Abdulkreem AL-Huqail, Hanan R. H. Mohamed and Ilaria Peluso

Plants 2022, 11(13), 1774; https://doi.org/10.3390/plants11131774 - 4 Jul 2022

Cited by 14 | Viewed by 2307

Abstract

Six mungbean parental lines and their fifteen F₁s produced from half-diallel mating design were investigated for combining ability and heterosis in terms of a yield and its components. Results showed highly significant variations among the parents and F₁s, suggesting [...] Read more.

Six mungbean parental lines and their fifteen F₁s produced from half-diallel mating design were investigated for combining ability and heterosis in terms of a yield and its components. Results showed highly significant variations among the parents and F₁s, suggesting a wide genetic variability for the studied characters. Analysis of variance indicated that genotypes mean square values, general combining ability (GCA) and specific combining ability (SCA) were highly significant (p ≤ 0.001) for all measured traits except for days to flowering, days to maturity, and pod length indicating genetic diversity of parents and both additive and non-additive gene effects in the inheritance of the measured traits. A higher effect of SCA than GCA for plant height and seeds per pod suggests the preponderance of non-additive gene effects in the expression of characters. Based on per se performance and GCA, BARI Mung-1, PS-7, and BMXK1-14004 were the best general combiners for yield per plant. In the context of SCA, hybrids BMXK1-14004 × Sonali mung, BMXK1-14004 × PS-7, BMXK1-14004 × BINA Mung-8, Sukumar × PS-7, and BARI Mung-1 × BINA Mung-8 were good specific combiners. BMXK1-14004 × Sonali mung and BMXK1-14004 × PS-7 were the best heterotic hybrids for yield and yield-contributing traits. These parents and crosses could be utilized for further use in breeding programs to improve yields in mungbean crops. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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25 pages, 3425 KiB

Open AccessArticle

Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping

by Priyadarsini Sanghamitra, Saumya Ranjan Barik, Ramakrushna Bastia, Shakti Prakash Mohanty, Elssa Pandit, Abhisarika Behera, Jyotirmayee Mishra, Gaurav Kumar and Sharat Kumar Pradhan

Plants 2022, 11(11), 1463; https://doi.org/10.3390/plants11111463 - 30 May 2022

Cited by 9 | Viewed by 1908

Abstract

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 [...] Read more.

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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13 pages, 3644 KiB

Open AccessArticle

Emmer Wheat Eco-Geographic and Genomic Congruence Shapes Phenotypic Performance under Mediterranean Climate

by Aviya Fadida-Myers, Dana Fuerst, Aviv Tzuberi, Shailesh Yadav, Kamal Nashef, Rajib Roychowdhury, Carolina Paola Sansaloni, Sariel Hübner and Roi Ben-David

Plants 2022, 11(11), 1460; https://doi.org/10.3390/plants11111460 - 30 May 2022

Cited by 5 | Viewed by 2447

Abstract

Emmer wheat (Triticum turgidum ssp. dicoccum) is one of the world’s oldest domesticated crops, and it harbors a potentially rich reservoir of agronomic and nutritional quality trait variations. The growing global demand for plant-based health-food niche markets has promoted new commercial [...] Read more.

Emmer wheat (Triticum turgidum ssp. dicoccum) is one of the world’s oldest domesticated crops, and it harbors a potentially rich reservoir of agronomic and nutritional quality trait variations. The growing global demand for plant-based health-food niche markets has promoted new commercial interest in ancient grains, including Emmer wheat. Although T. dicoccum can also perform well under harsh environments, its cultivation along the Mediterranean agro-ecosystems is sparse. Here, we analyze a unique tetraploid wheat collection (n = 121) representing a wide geographic range of Emmer accessions, using 9897 DArTseq markers and on-field phenotypic characterization to quantify the extent of diversity among populations and the interactions between eco-geographic, genetic, and phenotypic attributes. Population genomic inferences based on the DArTseq data indicated that the collection could be split into four distinguished clusters in accordance with their eco-geographic origin although significant phenotypic variation was observed within clusters. Superior early vegetative vigor, shorter plant height, and early phenology were observed among emmer wheat accessions from Ethiopia compared to accessions from northern regions. This adaptive advantage highlights the potential of emmer wheat as an exotic germplasm for wheat improvement through breeding. The direct integration of such germplasm into conventional or organic farming agro-systems under the Mediterranean basin climate is also discussed. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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26 pages, 6400 KiB

Open AccessArticle

Comparative Mutagenic Effectiveness and Efficiency of Gamma Rays and Sodium Azide in Inducing Chlorophyll and Morphological Mutants of Cowpea

by Aamir Raina, Rafiul Amin Laskar, Mohammad Rafiq Wani, Basit Latief Jan, Sajad Ali and Samiullah Khan

Plants 2022, 11(10), 1322; https://doi.org/10.3390/plants11101322 - 16 May 2022

Cited by 27 | Viewed by 4006

Abstract

Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing genetic diversity in crops. However, conclusive evidence of using an effective and efficient dose of gamma (γ) rays and sodium azide (SA) [...] Read more.

Mutagenic effectiveness and efficiency are the most important factors determining the success of mutation breeding, a coherent tool for quickly enhancing genetic diversity in crops. However, conclusive evidence of using an effective and efficient dose of gamma (γ) rays and sodium azide (SA) for genetic improvement is scant. The present study assesses genetic diversity in M₂ mutants of cowpea and evaluates mutagenic effectiveness and efficiency of the single and combination doses of γ rays and SA. In M₀ generation, 7200 M₁ seeds obtained by SA treatment (0.01—0.1%) and γ irradiation (100—1000 Gy) at a dose rate of 11.58 Gy/min were sown to raise M₁ generation. A total of 57,620 M₂ seeds were generated from the M₁ generation of two varieties—Gomati VU-89 and Pusa-578, from which 47,650 seeds germinated. Moreover, plants (38,749) that survived were screened for chlorophyll and morphological mutations. Among the mutagens, SA followed by γ rays + SA and γ rays was most effective in inducing higher frequency and a broader spectrum of chlorophyll mutants. A wide range of morphological mutants affecting every growth stage was recorded with the highest frequency in 400 Gy γ rays + 0.04% SA treatment. These morphological mutants with desirable agronomic traits represent a valuable genetic resource for future breeding programs. This study revealed the potency of γ rays and SA in increasing genetic diversity and demonstrated the successful conduct of induced mutagenesis in the cowpea. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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Review

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13 pages, 553 KiB

Open AccessReview

CRISPR/Cas Technology Revolutionizes Crop Breeding

by Qiaoling Tang, Xujing Wang, Xi Jin, Jun Peng, Haiwen Zhang and Youhua Wang

Plants 2023, 12(17), 3119; https://doi.org/10.3390/plants12173119 - 30 Aug 2023

Cited by 2 | Viewed by 4401

Abstract

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to [...] Read more.

Crop breeding is an important global strategy to meet sustainable food demand. CRISPR/Cas is a most promising gene-editing technology for rapid and precise generation of novel germplasm and promoting the development of a series of new breeding techniques, which will certainly lead to the transformation of agricultural innovation. In this review, we summarize recent advances of CRISPR/Cas technology in gene function analyses and the generation of new germplasms with increased yield, improved product quality, and enhanced resistance to biotic and abiotic stress. We highlight their applications and breakthroughs in agriculture, including crop de novo domestication, decoupling the gene pleiotropy tradeoff, crop hybrid seed conventional production, hybrid rice asexual reproduction, and double haploid breeding; the continuous development and application of these technologies will undoubtedly usher in a new era for crop breeding. Moreover, the challenges and development of CRISPR/Cas technology in crops are also discussed. Full article

(This article belongs to the Special Issue Advances in Genetics and Breeding of Grain Crops)

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