Agronomy

Editorial

Jump to: Research

7 pages, 1633 KiB

Open AccessEditorial

The Genetics, Genomics, and Breeding of Cereals and Grain Legumes: Traits and Technologies for Future Food Security

by Muhammad Amjad Nawaz, Gyuhwa Chung and Kirill S. Golokhvast

Agronomy 2023, 13(8), 2065; https://doi.org/10.3390/agronomy13082065 - 4 Aug 2023

Viewed by 1025

Abstract

According to the United Nations (UN), the world’s population is expected to grow by more than one billion people over the next 15 years [...] Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

Research

Jump to: Editorial

12 pages, 2080 KiB

Open AccessArticle

Inheritance of the Resistance to Acanthoscelides obtectus (Say.) in a Heterogeneous Inbred Families Population of Common Bean (Phaseolus vulgaris L.)

by Adriana Yuzaleth Ayala-Ruiz, Gloria Castellanos-Pérez, José Cruz Jiménez-Galindo, Nadiezhda Ramírez-Cabral, Orlando Ramírez-Valle, Juan José Figueroa-González and Rosa A. Malvar

Agronomy 2023, 13(10), 2553; https://doi.org/10.3390/agronomy13102553 - 4 Oct 2023

Viewed by 862

Abstract

The bean weevil Acanthoscelides obtectus is one of the world’s main pests of stored beans. The heterogeneous inbred family (HIF) population of near-isogenic lines (NILs) could be an exceptional strategy to study the inheritance of the resistance against A. obtectus. We developed [...] Read more.

The bean weevil Acanthoscelides obtectus is one of the world’s main pests of stored beans. The heterogeneous inbred family (HIF) population of near-isogenic lines (NILs) could be an exceptional strategy to study the inheritance of the resistance against A. obtectus. We developed a HIF population of 148 NILs of R-bufa-80-12. The objectives of this research were as follows: (1) to study and understand the genetics of the attack resistance to A. obtectus in a HIF population and (2) to identify the best lines to provide weevil resistance. The pure lines of the HIF population showed a great variability for all the analyzed traits. The traits studied in this research have a normal distribution showing continuous variation, so they are considered to be quantitatively inherited. The heritabilities for resistance traits were low and very low, ranging from 0.09 to 0.17. The heritability for 100 seed weight was the highest, with a significant value of 0.90. The best lines of the HIF population for resistance to A. obtectus comprised Line-45, Line-129, Line-124, Line-142 and Line-47. In general, these lines presented lower preference of adults, and lower consumption in grams and in percentages. However, lines 45 and 129 are the most interesting from a commercial point of view because they combine resistance and seed weight. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

19 pages, 3619 KiB

Open AccessArticle

Exploring the Agronomic Performance and Molecular Characterization of Diverse Spring Durum Wheat Germplasm in Kazakhstan

by Daniyar Tajibayev, Kadyrzhan Mukin, Adylkhan Babkenov, Vladimir Chudinov, Abdelfattah A. Dababat, Karlyga Jiyenbayeva, Serik Kenenbayev, Timur Savin, Vladimir Shamanin, Kuttymurat Tagayev, Askhat Rsymbetov, Minura Yessimbekova, Vadim Yusov, Ruslan Zhylkybaev, Alexey Morgounov, Muhammad Tanveer Altaf, Muhammad Azhar Nadeem and Faheem Shehzad Baloch

Agronomy 2023, 13(7), 1955; https://doi.org/10.3390/agronomy13071955 - 24 Jul 2023

Cited by 3 | Viewed by 1605

Abstract

Spring durum wheat occupies over 0.5 M ha in Kazakhstan and represents an important domestic and export commodity. This study aimed to characterize 151 durum wheat cultivars and advanced lines originating from eight breeding programs of the Kazakhstan–Siberia Spring Wheat Improvement Network (KASIB) [...] Read more.

Spring durum wheat occupies over 0.5 M ha in Kazakhstan and represents an important domestic and export commodity. This study aimed to characterize 151 durum wheat cultivars and advanced lines originating from eight breeding programs of the Kazakhstan–Siberia Spring Wheat Improvement Network (KASIB) between 2003 and 2018. The phenotypic characterization was performed in two contracting evaluation sites more than 1000 km apart (Almaty in the Southeast and Shortandy in the North) for two years and a total of 11 agronomic traits were recorded. Field trials at both locations followed regional agronomy practices, including sowing, harvesting, and genotype evaluation using a randomized complete block design (RCBD). The growing season was longer in Almaty, resulting in a higher number of grains per spike. Though grains are smaller in size with an overall higher yield, 243 g/m² versus 170 g/m², there was no correlation between germplasm performance at the two sites. Molecular characterization was performed with 10 iPBS-retrotransposons primers that resulted in a total of 345 bands and showed a mean polymorphism of 91.9%. Mean values of gene diversity (0.251), Shannon’s information index (0.388), and expected heterozygosity (0.233) revealed a relatively high level of genetic diversity in the KASIB set. AMOVA revealed higher genetic variations due to differences within the populations. Marker-based cluster analysis, including STRUCTURE and neighbor-joining algorithms, divided the material into two populations with clear differences in geographic origin. Superiors and diverse germplasm identified in the study are recommended for marker assisted selection and breeding. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

23 pages, 4122 KiB

Open AccessArticle

Comparative Omics-Based Identification and Expression Analysis of a Two-Component System in Vigna radiata in Drought Stress

by Muhammad Amin Afzal, Farrukh Azeem, Shumaila Afzal, Naila Afzal, Muhammad Rizwan, Hyojin Seo, Asad Ali Shah and Muhammad Amjad Nawaz

Agronomy 2023, 13(4), 989; https://doi.org/10.3390/agronomy13040989 - 27 Mar 2023

Cited by 2 | Viewed by 1301

Abstract

Two-component system (TCS) genes regulate a wide range of biological activities in prokaryotes and eukaryotes, including plants. TCS plays an important role in cellular responses to external stimuli, such as biotic and abiotic factors. In plants, this system supports cell division, leaf senescence, [...] Read more.

Two-component system (TCS) genes regulate a wide range of biological activities in prokaryotes and eukaryotes, including plants. TCS plays an important role in cellular responses to external stimuli, such as biotic and abiotic factors. In plants, this system supports cell division, leaf senescence, stress response, chloroplast division, and nutrient signaling. There are three kinds of proteins responsible for the appropriate functioning of the TCS system: histidine kinases (HKs), histidine phosphotransfer proteins (HPs), and response regulators (RRs). The results of the current study revealed that Vigna radiata has 54 genes encoding potential TCS proteins, which were divided into three subgroups: 18 HKs, 9 HPs (seven true and two pseudos), and 27 RRs (8 type-A, 8 type-B, 3 type-C, and 8 PRRS). The anticipated TCS genes were widely dispersed across all eleven chromosomes and had family-specific intron/exon structures. After investigating TCS genes in a variety of plant species, we determined that Vigna HK (L)s, HPs, and RRs have closer evolutionary relationships with other legume genes. Gene duplication, including segmental and tandem types, is the most frequent source of gene family expansion. Multiple stress-related cis-elements were predicted in the promoter sequences of the VrTCS genes. RNA-seq data analysis demonstrated that VrTCS genes were expressed in clusters of upregulated and downregulated groups in response to drought stress. Moreover, these clusters were differentially expressed as early or late responses to drought stress. Real-time qPCR showed that VrHK2, VrHK3, VrPHYE, VrHP4.1, VrRR5.2, and VrRR10 genes were upregulated, while VrRR3 and VrHP6.1 genes were downregulated in response to drought stress. The current study highlights the architecture of V. radiata TCS and provides a robust framework for subsequent functional evaluation. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

13 pages, 1353 KiB

Open AccessArticle

Genetic Diversity of Global Faba Bean Germplasm Resources Based on the 130K TNGS Genotyping Platform

by Hongyan Zhang, Yujiao Liu, Xuxiao Zong, Changcai Teng, Wanwei Hou, Ping Li and Dezhi Du

Agronomy 2023, 13(3), 811; https://doi.org/10.3390/agronomy13030811 - 10 Mar 2023

Cited by 4 | Viewed by 1696

Abstract

Novel germplasm resources are the key to crop breeding, with their genetic diversity and population structure analysis being highly significant for future faba bean breeding. We genotyped 410 global faba bean accessions using the 130K targeted next-generation sequencing (TNGS) genotyping platform, resulting in [...] Read more.

Novel germplasm resources are the key to crop breeding, with their genetic diversity and population structure analysis being highly significant for future faba bean breeding. We genotyped 410 global faba bean accessions using the 130K targeted next-generation sequencing (TNGS) genotyping platform, resulting in a total of 38,111 high-quality SNP loci by high-standard filtering. We found the polymorphism information content (PIC) and Nei’s gene diversity were 0.0905–0.3750 and 0.0950–0.5000, with averages of 0.2471 and 0.3035, respectively. After evaluating the genetic diversity of 410 accessions using Nei’s gene diversity and PIC, on the basis of their geographical origin (continent) and structure-analysis-inferred subpopulations, we found that the faba bean accessions from Asia (except China) and Europe had rich genetic diversity, while those from the winter sowing area of China were low. The 410 faba bean accessions were divided into four subpopulations according to population structure analysis and clustering analysis based on Nei’s (1972) genetic distance using the neighbor-joining (NJ) method. However, the same subpopulation contained materials from different geographical origins, thereby indicating that the gene flow or introgression occurred among the accessions. Results from NJ clustering based on shared allele genetic distance indicated that the 410 accessions were divided into three groups according to their dissemination routes. The genetic diversity analysis results demonstrated that the genetic relationships among the faba bean groups with similar ecological environments and geographic origins in neighboring regions or countries were closer and frequently found within the same group, while genetic variation among individuals was the main source of their total genetic variation. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

32 pages, 4212 KiB

Open AccessArticle

Association Mapping for Quantitative Trait Loci Controlling Superoxide Dismutase, Flavonoids, Anthocyanins, Carotenoids, γ-Oryzanol and Antioxidant Activity in Rice

by Ramakrushna Bastia, Elssa Pandit, Priyadarsini Sanghamitra, Saumya Ranjan Barik, Deepak Kumar Nayak, Auromira Sahoo, Arpita Moharana, Jitendriya Meher, Prasanta K. Dash, Reshmi Raj, Binod Kumar Jena, Kartik Chandra Pradhan, Devraj Lenka, Nabaneeta Basak, Srikanta Lenka and Sharat Kumar Pradhan

Agronomy 2022, 12(12), 3036; https://doi.org/10.3390/agronomy12123036 - 30 Nov 2022

Cited by 9 | Viewed by 1552

Abstract

Antioxidant-rich rice is a cheaper way to solve stress-related disorders and other health benefits for the global rice-eating population. Five antioxidant traits, namely, superoxide dismutase, flavonoids, anthocyanins, γ-oryzanol and 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) activity were mapped using a representative panel population through association mapping. [...] Read more.

Antioxidant-rich rice is a cheaper way to solve stress-related disorders and other health benefits for the global rice-eating population. Five antioxidant traits, namely, superoxide dismutase, flavonoids, anthocyanins, γ-oryzanol and 2,2′-azino-bis-3-ethylbenzthiazoline-6-sulphonic acid (ABTS) activity were mapped using a representative panel population through association mapping. Potential landraces carrying multiple antioxidant compounds were identified from the population. The population represented four genetic groups and correspondence for presence of antioxidants traits in each group was noticed. The population showed linkage disequilibrium for the studied traits based on the Fst values. A total of 14 significant marker–trait associations were detected for these antioxidant traits. The study validated the QTLs, qANC3 and qPAC12-2 for anthocyanin content and qAC12 for ABTS activity will be useful in marker-assisted breeding. Eleven QTLs such as qTAC1.1 and qTAC5.1 controlling anthocyanin content, qSOD1.1, qSOD5.1 and qSOD10.1 for superoxide dismutase (SOD), qTFC6.1, qTFC11.1 and qTFC12.1 for total flavonoids content (TFC), qOZ8.1 and qOZ11.1 for γ-oryzanol (OZ) and qAC11.1 for ABTS activity were detected as novel loci. Chromosomal locations on 11 at 45.3 cM regulating GO, TFC and TAC, and on the chromosome 12 at 101.8 cM controlling TAC and ABTS activity, respectively, were detected as antioxidant hotspots. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Graphical abstract

12 pages, 1114 KiB

Open AccessArticle

Comparative Analysis of Pedigree-Based BLUP and Phenotypic Mass Selection for Developing Elite Inbred Lines, Based on Field and Simulated Data

by José Marcelo Soriano Viana, Kaio Olimpio das Graças Dias and Jean Paulo Aparecido da Silva

Agronomy 2022, 12(10), 2560; https://doi.org/10.3390/agronomy12102560 - 19 Oct 2022

Cited by 2 | Viewed by 1507

Abstract

Pedigree-based best linear unbiased prediction (pBLUP) is an effective method for genetic evaluation. The objective of this study was to assess the efficacy of pBLUP to develop superior inbred lines, using field and simulated data. This study was based on the data of [...] Read more.

Pedigree-based best linear unbiased prediction (pBLUP) is an effective method for genetic evaluation. The objective of this study was to assess the efficacy of pBLUP to develop superior inbred lines, using field and simulated data. This study was based on the data of 30,986 plants from six S₀ generations and eight inbred progeny trials (S₁–S₄), performed over eight years. We measured the grain yield and the expansion volume (EV). We also simulated the EV and grain yield of 5000 plants (S₀–S₄) in two in silico populations, assuming 300 and 400 genes distributed across 10 chromosomes of 200 cM, respectively, and 10% of pleiotropic genes. We selected selfed plants based on the predicted additive value for EV by fitting the individual model in inbred population. The use of pBLUP provided total genetic gains in EV in the range of 1 to 45%, inversely proportional to the level of improvement of the population, and indirect changes in grain yield in the range of −17 to 3%. Only from the analysis of the in silico populations, assuming selection based on the true additive value and genetic gain computed from the genotypic values, there was evidence that pBLUP is superior to phenotypic mass selection. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures

Figure 1

13 pages, 2021 KiB

Open AccessArticle

Alternative Splicing (AS) Dynamics in Dwarf Soybean Derived from Cross of Glycine max and Glycine soja

by Neha Samir Roy, Prakash Basnet, Rahul Vasudeo Ramekar, Taeyoung Um, Ju-Kyung Yu, Kyong-Cheul Park and Ik-Young Choi

Agronomy 2022, 12(7), 1685; https://doi.org/10.3390/agronomy12071685 - 16 Jul 2022

Cited by 2 | Viewed by 1696

Abstract

Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf [...] Read more.

Short crop height is the preferred breeding trait since there is a positive correlation between lodging resistance and a crop yield increase. Alternative splicing can alter transcriptome diversity and contribute to plant adaptation to environmental stress. We characterized the transcriptomes obtained from dwarf and normal soybean lines derived from a cross of Glycine max var. Peking (G. max) and G. soja var. IT182936 in an F7 RIL population to study the differences between the isoforms. Full-length mRNA derived from leaf tissues was sequenced using the PacBio RSII platform, generating 904,474 circular consensus sequence (CCS) reads. Using the Structural and Quality Annotation of Novel Transcript Isoforms (SQANTI) process, 42,582 and 44,762 high-quality isoforms, and 91 and 179 polished low-quality isoforms were obtained in dwarf and normal cells, respectively. As a result, 832 and 36,772 nonredundant transcripts were generated. Approximately 30% of the identified genes were estimated to produce two or more isoforms. We detected an average of 166,171 splice junctions (SJs), of which 93.8% were canonical SJs. We identified that novel isoforms accounted for 19% of all isoforms, among which 12% fell within coding regions. The dwarf soybean demonstrated a greater number of isoforms in most of the annotated genes, particularly in genes related to growth hormones and defense responses. Our study provides comprehensive isoform and gene information that may accelerate transcriptome research in G. max and provide a basis to further study the impact of these isoforms on plant growth. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Cereals and Grain Legumes)

► Show Figures