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20 pages, 2553 KiB

Open AccessArticle

Molecular Characterization and Haplotype Analysis of Low Phytic Acid-1 (lpa1) Gene Governing Accumulation of Kernel Phytic Acid in Subtropically-Adapted Maize

by Vinay Bhatt, Vignesh Muthusamy, Rashmi Chhabra, Ashvinkumar Katral, Shridhar Ragi, Vinay Rojaria, Gulab Chand, Govinda Rai Sarma, Rajkumar Uttamrao Zunjare, Kusuma Kumari Panda, Ashok Kumar Singh and Firoz Hossain

Agriculture 2023, 13(7), 1286; https://doi.org/10.3390/agriculture13071286 - 22 Jun 2023

Viewed by 1317

Abstract

Maize is an important food, feed, fodder and industrial crop in addition to being a valuable source of micronutrients. Phytic acid (PA), an anti-nutritional factor in maize, makes crucial minerals inaccessible to monogastric animals. The low phytic acid-1 (lpa1) gene located [...] Read more.

Maize is an important food, feed, fodder and industrial crop in addition to being a valuable source of micronutrients. Phytic acid (PA), an anti-nutritional factor in maize, makes crucial minerals inaccessible to monogastric animals. The low phytic acid-1 (lpa1) gene located on chromosome-1S is 7292 bp long with 11 exons, and the recessive lpa1-1 allele reduces the accumulation of PA thereby enhances the bioavailability of essential minerals in maize kernels. Here, we characterized the full-length Lpa1 gene sequence in three mutants (lpa1-1) and seven wild-type (Lpa1) maize inbreds. Sequence analysis revealed 607 polymorphic sites across Lpa1 sequences, indicating wide variability for Lpa1 among the inbreds. Further, SNP from “C” to “T” differentiated wild-type and mutant-type alleles at 1432 amino acid position. Gene-based diversity among 48 diverse maize inbreds using 15 InDel markers revealed the formation of 42 distinct haplotypes; six of which (Hap6, Hap16, Hap17, Hap19 Hap27 and Hap31) were shared by more than one genotype. The number of exons in Lpa1 ranged from 11–19 among maize genotypes and 6–14 among 26 orthologues. Major functional motifs of Lpa1 detected were ATP-binding Cassette (ABC) transporter trans-membrane region and ABC transporter. Phylogenetic tree using nucleotide and protein sequences revealed a closer relationship of maize Lpa1 sequences with Sorghum bicolor, Panicum hallii, Setaria italica and S. viridis. This study offered newer insights into the understanding of the genetic diversity of the Lpa1 gene in maize and related crop-species, and information generated here would further help in exploiting the lpa1 mutant for the enhancement of nutritional value in maize kernels. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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13 pages, 1333 KiB

Open AccessArticle

Genetic Diversity and Population Structure Analysis to Construct a Core Collection from Safflower (Carthamus tinctorius L.) Germplasm through SSR Markers

by Gaddam Prasanna Kumar, Pooja Pathania, Nitu Goyal, Nishu Gupta, R. Parimalan, J. Radhamani, Sunil Shriram Gomashe, Palchamy Kadirvel and S. Rajkumar

Agriculture 2023, 13(4), 836; https://doi.org/10.3390/agriculture13040836 - 6 Apr 2023

Cited by 5 | Viewed by 1972

Abstract

Genetic resources are the fundamental source of diversity available to plant breeders for the improvement of desired traits. However, a large germplasm set is difficult to preserve and use as a working collection in genetic studies. Hence, the present study evaluates the genetic [...] Read more.

Genetic resources are the fundamental source of diversity available to plant breeders for the improvement of desired traits. However, a large germplasm set is difficult to preserve and use as a working collection in genetic studies. Hence, the present study evaluates the genetic diversity of 3115 safflower accessions from the Indian National Gene Bank, including Indian cultivars, to develop a manageable set of accessions, with similar genetic variations of germplasm studied. A total of 18 polymorphic SSR markers were used. The genetic diversity analysis revealed that germplasm accessions were highly diverse and there is no correlation between genetic diversity and the geographical collection of germplasm or sourcing of germplasm. A core set was developed using a core hunter software with different levels of composition, and it was found that 10% of the accessions showed maximum gene diversity and represented an equal number of alleles and major allele frequency in the germplasm studied. The developed core consisted of 351 accessions, including Indian cultivars, and they were validated with various genetic parameters to ascertain that they were a true core set for the studied accessions of safflower germplasm. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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17 pages, 3850 KiB

Open AccessArticle

SSR and SNP Marker-Based Investigation of Indian Rice Landraces in Relation to Their Genetic Diversity, Population Structure, and Geographical Isolation

by Debjani Roy Choudhury, Ramesh Kumar, Avantika Maurya, Dinesh P. Semwal, Ranbir S. Rathi, Raj K. Gautam, Ajaya K. Trivedi, Santosh K. Bishnoi, Sudhir P. Ahlawat, Kuldeep Singh, Nagendra K. Singh and Rakesh Singh

Agriculture 2023, 13(4), 823; https://doi.org/10.3390/agriculture13040823 - 3 Apr 2023

Cited by 4 | Viewed by 2581

Abstract

India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions [...] Read more.

India is blessed with an abundance of diverse rice landraces in its traditional cultivated areas. Two marker systems (simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)) were used to study a set of 298 rice landrace accessions collected from six different regions of India (Andaman and Nicobar Islands, Chhattisgarh, Jharkhand, Uttar Pradesh, Uttarakhand, and West Bengal). Thirty hyper-variable simple sequence repeats (HvSSRs) and 32,782 single nucleotide polymorphisms (SNPs) were used in inferring genetic structure and geographical isolation. Rice landraces from Uttar Pradesh were the most diverse, with a gene diversity value of 0.42 and 0.49 with SSR and SNP markers, respectively. Neighbor-joining trees classified the rice landraces into two major groups with SSR and SNP markers, and complete geographical isolation was observed with SSR markers. Fast STRUCTURE analysis revealed four populations for SSR markers and three populations for SNP markers. The population structure with SSR markers showed that few individuals from Uttarakhand and Andaman and Nicobar Islands were grouped in small clusters. Population structure analysis with SNP markers showed not very distinct region-wise clustering among the rice landraces. Discriminant analysis of principal components (DAPC) and minimum spanning network (MSN) using SSR markers showed region-wise grouping of landraces with some intermixing, but DAPC and MSN with SNP markers showed very clear region-wise clustering. Genetic differentiation of rice landraces between the regions was significant with both SSR (Fst 0.094–0.487) and SNP markers (Fst 0.047–0.285). A Mantel test revealed a positive correlation between the genetic and geographic distance of rice landraces. The present study concludes that rice landraces investigated in this study were very diverse, and unlinked SSR markers show better geographical isolation than a large set of SNP markers. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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15 pages, 533 KiB

Open AccessArticle

Developing an NIRS Prediction Model for Oil, Protein, Amino Acids and Fatty Acids in Amaranth and Buckwheat

by Shruti, Alka Shukla, Saman Saim Rahman, Poonam Suneja, Rashmi Yadav, Zakir Hussain, Rakesh Singh, Shiv Kumar Yadav, Jai Chand Rana, Sangita Yadav and Rakesh Bhardwaj

Agriculture 2023, 13(2), 469; https://doi.org/10.3390/agriculture13020469 - 16 Feb 2023

Cited by 2 | Viewed by 1858

Abstract

Amaranth and buckwheat are two pseudo-cereals preferred for their high nutritional value, are gluten free and carry religious importance as fasting food. Germplasm resources are the reservoir of diversity for different traits, including nutritional characteristics. These resources must be evaluated to utilize their [...] Read more.

Amaranth and buckwheat are two pseudo-cereals preferred for their high nutritional value, are gluten free and carry religious importance as fasting food. Germplasm resources are the reservoir of diversity for different traits, including nutritional characteristics. These resources must be evaluated to utilize their potential in crop improvement programs. However, conventional methods are labor-, cost- and time-intensive and prone to handling errors when applied to large samples. NIRS-based machine learning to predict different nutritional traits is applied in different food crops for multiple traits. NIRS prediction models are developed in this study using the mPLS regression technique for oil, protein, fatty acids and essential amino acid estimation in amaranth and buckwheat. Good RSQ external (power of determination) values were obtained for the above traits ranging from 0.72 to 0.929. Ratio performance deviation (RPD) value for most of the traits ranged between 2 and 3, except for valine (1.88) and methionine (3.55), indicating good prediction capabilities in the developed model. These prediction models were utilized in screening the germplasm of amaranth and buckwheat; the results obtained were in good agreement and confirmed the applicability of developed models. It will enable the identification of a trait-specific germplasm as a potential gene source and aid in crop improvement programs. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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14 pages, 2717 KiB

Open AccessArticle

Validation of Genome-Wide SSR Markers Developed for Genetic Diversity and Population Structure Study in Grain Amaranth (Amaranthus hypochondriacus)

by Gautam Vats, Dimpi Das, Rajat Gupta, Akshay Singh, Avantika Maurya, S. Rajkumar, Amit Kumar Singh, Rakesh Bharadwaj, Sandeep Kumar, Surinder Kumar Kaushik, Veena Gupta, Kuldeep Singh and Rakesh Singh

Agriculture 2023, 13(2), 431; https://doi.org/10.3390/agriculture13020431 - 12 Feb 2023

Cited by 4 | Viewed by 2453

Abstract

Grain Amaranth is the most promising C₄ dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized [...] Read more.

Grain Amaranth is the most promising C₄ dicotyledonous pseudocereal and is distributed globally. It has an excellent nutritional profile and adaptability against a broad range of environmental factors. These traits have renewed the interest of researchers and breeders in exploring this underutilized orphan crop. The present study aimed to validate the genome-wide SSR to assess the genetic diversity among 94 Amaranthus hypochondriacus accessions using 57 genomic SSR (g-SSR) markers developed in-house. A total of 36 g-SSRs were recorded as polymorphic and amplified 138 alleles, with an average of 3.83 alleles per locus. Major allele frequency ranged from 0.29 to 0.98, with an average of 0.63 per marker. The expected heterozygosity ranged from 0.03 to 0.81, with an average of 0.46 per locus. Polymorphism information content (PIC) ranged from 0.03 to 0.79, with an average of 0.40, indicating a high level of polymorphism across amaranth accessions. Population structure analysis resulted into two major genetic clusters irrespective of their geographical origin, which suggests there may be sharing of common genomic regions across the accessions. High allelic frequency and heterozygosity levels indicate significant genetic variability in the germplasm, which can be further used in future breeding programs. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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20 pages, 3132 KiB

Open AccessArticle

Identification and Analysis of Phosphatidylethanolamine-Binding Protein Family Genes in the Hangzhou White Chrysanthemum (Chrysanthemum morifolium Ramat)

by Cheng Pan, Xueyi He, Shiyue Song, Liping Zou, Mengxin Wang and Baoyu Han

Agriculture 2023, 13(2), 374; https://doi.org/10.3390/agriculture13020374 - 4 Feb 2023

Cited by 1 | Viewed by 1627

Abstract

The Hangzhou White Chrysanthemum (Chrysanthemum morifolium Ramat) is one of the “Zhejiang eight flavors” in traditional Chinese medicine. The phosphatidylethanolamine-binding protein (PEBP) plays an important role in flowering and floral organ development. Even so, the biological role of PEBPs in the Hangzhou [...] Read more.

The Hangzhou White Chrysanthemum (Chrysanthemum morifolium Ramat) is one of the “Zhejiang eight flavors” in traditional Chinese medicine. The phosphatidylethanolamine-binding protein (PEBP) plays an important role in flowering and floral organ development. Even so, the biological role of PEBPs in the Hangzhou White Chrysanthemum has not been studied, which attracted us. Here, nine CmPEBP genes that contain the PF01161 domain were identified in the Hangzhou White Chrysanthemum for the first time, and their biological role in flowering was preliminarily studied. A phylogenetic analysis classified the CmPEBP genes into three subfamilies: MFT-like, TFL-like, and FT-like genes. The differential expression analysis was performed under different tissues and different stressors using qRT-PCR. It showed that each CmPEBP displayed tissue-specific expression patterns. Expression patterns in response to different temperatures and hormone stressors were investigated. They were finally demonstrated to be differentially expressed. TFL-like gene expression, which delayed reproductive growth, was upregulated under heat stress. Conversely, FT-like gene expression was upregulated under low temperatures. CmFT1 expression could be inhibited by GA (gibberellin), 6-BA (benzylaminopurine), ET (ethylene), and MeSA (methyl salicylate) but could be activated by IAA (indole-3-aceticacid), ABA (abscisic acid), and SA (salicylic acid) in the dark, whereas CmFT2 and CmFT3 expression levels were upregulated by ET, MeJA (methyl jasmonate), and ABA but were downregulated by 6-BA, SA, and MeSA. GA, IAA, SA, and MeSA inhibited CmTFL gene expression under light and dark treatments. Further research on CmPEBP genes in the Hangzhou White Chrysanthemum could better determine their roles in flowering and floral organ development, especially in response to the prolonged spraying of exogenous hormones. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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23 pages, 4496 KiB

Open AccessArticle

Genome-Wide Identification and Characterization of Trihelix Gene Family in Asian and African Vigna Species

by Shweta Kumari, Dhammaprakash Pandhari Wankhede, Sneha Murmu, Ranjeet Maurya, Sarika Jaiswal, Anil Rai and Sunil Archak

Agriculture 2022, 12(12), 2172; https://doi.org/10.3390/agriculture12122172 - 18 Dec 2022

Viewed by 1845

Abstract

Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of crops has different [...] Read more.

Trihelix transcription factors play a crucial role in varied stress responses as well as in the growth and development of plants. The role of trihelix transcription factors in the non-shattering phenotype in domesticated rice is known. The Vigna group of crops has different degrees of shattering phenotypes in different species. To understand the evolutionary conservation or divergence of the trihelix gene family in important Vigna species here, the genome-wide identification and characterization of the trihelix gene family in four Vigna species including the cowpea (Vigna unguiculata), mung bean (V. radiata), adzuki bean (V. angularis) and rice bean (V. umbellata) was performed. A total of 39, 35, 41 and 50 trihelix genes were identified in the cowpea, mung bean, adzuki bean and rice bean, respectively. The trihelix genes in each of the four Vigna species were classified into five subgroups: GT, GTγ, SH4, S1P1 and GTδ. The members of each subgroup shared similar patterns of gene structure and motif across the four species. The cross-species positional relationships of the cowpea, adzuki bean and mung bean vis-a-vis rice trihelix genes were studied. Further, the Ka/Ks ratio for the trihelix genes in the four Vigna species indicated the purifying or stabilizing selection of the family. The gene expression analysis of the trihelix gene family in the cowpea showed that most of the genes express in at least some of the seed and/or pod developmental stages, although at varying degrees. Based on detailed bioinformatic analysis, a potential target for gene editing towards a possible non-shattering phenotype in the four important Vigna crops was discussed. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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15 pages, 2208 KiB

Open AccessArticle

Comprehensive Evaluation of Morpho-Physiological and Ionic Traits in Wheat (Triticum aestivum L.) Genotypes under Salinity Stress

by Shiksha Chaurasia, Arvind Kumar and Amit Kumar Singh

Agriculture 2022, 12(11), 1765; https://doi.org/10.3390/agriculture12111765 - 25 Oct 2022

Cited by 5 | Viewed by 2017

Abstract

Salinity is the foremost abiotic stress that severely affects plant growth and constrains its productivity worldwide. In the present investigation, genetic variation in wheat genotypes was evaluated to identify novel salt-tolerant genetic resources, which could be used in the bread wheat improvement program. [...] Read more.

Salinity is the foremost abiotic stress that severely affects plant growth and constrains its productivity worldwide. In the present investigation, genetic variation in wheat genotypes was evaluated to identify novel salt-tolerant genetic resources, which could be used in the bread wheat improvement program. A diverse panel of 44 different wheat genotypes was evaluated at seedling stage to characterize morphological and ionic traits under salt stress (150 mM NaCl). Salt treatment caused 33.33, 45.31, 55.17, and 72.53% reduction in root dry weight (RDW), root fresh weight (RFW), shoot dry weight (SDW), and shoot fresh weight (SFW), respectively. Under salt stress, maximum inhibition of Na⁺ ion uptake was observed in tolerant genotypes, and this was accompanied by a high Ca²⁺ uptake. Wheat genotypes showed a wide spectrum of responses under salt stress; however, four genotypes, EC576356, IC533596, IC279230, and IC290188, exhibited consistent performance, which was strongly linked to proper Na⁺ and K⁺ discrimination in leaves. The tolerant genotypes acquired a better ability to maintain stable relative water content (RWC), chlorophyll (CHL), and photosynthesis rate (PS), resulting in significantly higher dry matter production under salt stress. Further, biomass, shoot K⁺, root Ca²⁺, and shoot K⁺/Na⁺ were identified as the most effective parameters for screening wheat germplasm for salinity tolerance. The identified germplasm could be used as donors for transferring salt tolerance to improved cultivars as well as in further genetic studies to uncover the genetic mechanisms governing salt stress response in wheat. Full article

(This article belongs to the Special Issue Breeding, Genetics and Genomics to Enhance Crop Production, towards Global Food Security)

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