Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration

Unlocking the nutritional potential of chickpea: strategies for biofortification and enhanced multinutrient quality

Chickpea (Cicer arietinum L.) is a vital grain legume, offering an excellent balance of protein, carbohydrates, fats, fiber, essential micronutrients, and vitamins that can contribute to addressing the global population's increasing food and nutritional demands. Chickpea protein offers a balanced source of amino acids with high bioavailability. Moreover, due to its balanced nutrients and affordable price, chickpea is an excellent alternative to animal protein, offering a formidable tool for combating hidden hunger and malnutrition, particularly prevalent in low-income countries. This review examines chickpea's nutritional profile, encompassing protein, amino acids, carbohydrates, fatty acids, micronutrients, vitamins, antioxidant properties, and bioactive compounds of significance in health and pharmaceutical domains. Emphasis is placed on incorporating chickpeas into diets for their myriad health benefits and nutritional richness, aimed at enhancing human protein and micronutrient nutrition. We discuss advances in plant breeding and genomics that have facilitated the discovery of diverse genotypes and key genomic variants/regions/quantitative trait loci contributing to enhanced macro- and micronutrient contents and other quality parameters. Furthermore, we explore the potential of innovative breeding tools such as CRISPR/Cas9 in enhancing chickpea's nutritional profile. Envisioning chickpea as a nutritionally smart crop, we endeavor to safeguard food security, combat hunger and malnutrition, and promote dietary diversity within sustainable agrifood systems.

Physical Seed Dormancy in Legumes: Molecular Advances and Perspectives

Physical dormancy of seeds is a form of dormancy due to the presence of an impermeable seed coat layer, and it represents a feature for plants to adapt to environmental changes over an extended period of phylogenetic evolution. However, in agricultural practice, physical dormancy is problematic. because it prevents timely and uniform seed germination. Therefore, physical dormancy is an important agronomical trait to target in breeding and domestication, especially for many leguminous crops. Compared to the well-characterized physiological dormancy, research progress on physical dormancy at the molecular level has been limited until recent years, due to the lack of suitable research materials. This review focuses on the structure of seed coat, factors affecting physical dormancy, genes controlling physical dormancy, and plants suitable for studying physical dormancy at the molecular level. Our goal is to provide a plethora of information for further molecular research on physical dormancy.

Assessment of yield performances for grain sorghum varieties by AMMI and GGE biplot analyses

Grain sorghum is an exceptional source of dietary nutrition with outstanding economic values. Breeding of grain sorghum can be slowed down by the occurrence of genotype × environment interactions (GEI) causing biased estimation of yield performance in multi-environments and therefore complicates direct phenotypic selection of superior genotypes. Multi-environment trials by randomized complete block design with three replications were performed on 13 newly developed grain sorghum varieties at seven test locations across China for two years. Additive main effects and multiplicative interaction (AMMI) and genotype + genotype × environment (GGE) biplot models were adopted to uncover GEI patterns and effectively identify high-yielding genotypes with stable performance across environments. Yield (YLD), plant height (PH), days to maturity (DTM), thousand seed weight (TSW), and panicle length (PL) were measured. Statistical analysis showed that target traits were influenced by significant GEI effects (p < 0.001), that broad-sense heritability estimates for these traits varied from 0.40 to 0.94 within the medium to high range, that AMMI and GGE biplot models captured more than 66.3% of total variance suggesting sufficient applicability of both analytic models, and that two genotypes, G3 (Liaoza No.52) and G10 (Jinza 110), were identified as the superior varieties while one genotype, G11 (Jinza 111), was the locally adapted variety. G3 was the most stable variety with highest yielding potential and G10 was second to G3 in average yield and stability whereas G11 had best adaptation only in one test location. We recommend G3 and G10 for the production in Shenyang, Chaoyang, Jinzhou, Jinzhong, Yulin, and Pingliang, while G11 for Yili.

Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm

Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.

Ensuring Global Food Security by Improving Protein Content in Major Grain Legumes Using Breeding and 'Omics' Tools

Grain legumes are a rich source of dietary protein for millions of people globally and thus a key driver for securing global food security. Legume plant-based 'dietary protein' biofortification is an economic strategy for alleviating the menace of rising malnutrition-related problems and hidden hunger. Malnutrition from protein deficiency is predominant in human populations with an insufficient daily intake of animal protein/dietary protein due to economic limitations, especially in developing countries. Therefore, enhancing grain legume protein content will help eradicate protein-related malnutrition problems in low-income and underprivileged countries. Here, we review the exploitable genetic variability for grain protein content in various major grain legumes for improving the protein content of high-yielding, low-protein genotypes. We highlight classical genetics-based inheritance of protein content in various legumes and discuss advances in molecular marker technology that have enabled us to underpin various quantitative trait loci controlling seed protein content (SPC) in biparental-based mapping populations and genome-wide association studies. We also review the progress of functional genomics in deciphering the underlying candidate gene(s) controlling SPC in various grain legumes and the role of proteomics and metabolomics in shedding light on the accumulation of various novel proteins and metabolites in high-protein legume genotypes. Lastly, we detail the scope of genomic selection, high-throughput phenotyping, emerging genome editing tools, and speed breeding protocols for enhancing SPC in grain legumes to achieve legume-based dietary protein security and thus reduce the global hunger risk.

The genetics of vigour-related traits in chickpea (Cicer arietinum L.): insights from genomic data

QTL controlling vigour and related traits were identified in a chickpea RIL population and validated in diverse sets of germplasm. Robust KASP markers were developed for marker-assisted selection. To understand the genetic constitution of vigour in chickpea (Cicer arietinum L.), genomic data from a bi-parental population and multiple diversity panels were used to identify QTL, sequence-level haplotypes and genetic markers associated with vigour-related traits in Australian environments. Using 182 Recombinant Inbred Lines (RILs) derived from a cross between two desi varieties, Rupali and Genesis836, vigour QTL independent of flowering time were identified on chromosomes (Ca) 1, 3 and 4 with genotypic variance explained (GVE) ranging from 7.1 to 28.8%. Haplotype analysis, association analysis and graphical genotyping of whole-genome re-sequencing data of two diversity panels consisting of Australian and Indian genotypes and an ICRISAT Chickpea Reference Set revealed a deletion in the FTa1-FTa2-FTc gene cluster of Ca3 significantly associated with vigour and flowering time. Across the RIL population and diversity panels, the impact of the deletion was consistent for vigour but not flowering time. Vigour-related QTL on Ca4 co-located with a QTL for seed size in Rupali/Genesis836 (GVE = 61.3%). Using SNPs from this region, we developed and validated gene-based KASP markers across different panels. Two markers were developed for a gene on Ca1, myo -inositol monophosphatase (CaIMP), previously proposed to control seed size, seed germination and seedling growth in chickpea. While associated with vigour in the diversity panels, neither the markers nor broader haplotype linked to CaIMP was polymorphic in Rupali/Genesis836. Importantly, vigour appears to be controlled by different sets of QTL across time and with components which are independent from phenology.

Genome resequencing reveals DNA polymorphisms associated with seed size/weight determination in chickpea

Crop productivity in legumes is determined by number and size/weight of seeds. To understand the genetic basis of seed size/weight in chickpea, we performed genome resequencing of 13 small- and 5 large-seeded genotypes using Illumina platform. Single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) differentiating small- and large-seeded genotypes were identified. A total of 17,902 SNPs and 2594 InDels located in promoter and/or coding regions that may contribute to seed size/weight were detected. Of these, 266 SNPs showed significant association with seed size/weight trait. Twenty-three genes including those involved in cell growth/division, encoding transcription factors and located within QTLs associated with seed size/weight harbored SNPs within transcription factor binding motif(s) and/or coding region. The non-synonymous SNPs were found to affect the mutational sensitivity and stability of the encoded proteins. Overall, we provided a high-quality SNP map for large-scale genotyping applications and identified candidate genes that determine seed size/weight in chickpea.

A high-density SNP-based linkage map using genotyping-by-sequencing and its utilization for improved genome assembly of chickpea (Cicer arietinum L.)

Genotyping-by-sequencing (GBS) allows rapid identification of markers for use in development of linkage maps, which expedite efficient breeding programs. In the present study, we have utilized GBS approach to identify and genotype single-nucleotide polymorphism (SNP) markers in an inter-specific RIL population of Cicer arietinum L. X C. reticulatum. A total of 141,639 raw SNPs were identified using the TASSEL-GBS pipeline. After stringent filtering, 8208 candidate SNPs were identified of which ~ 37% were localized in the intragenic regions followed by genic regions (~ 30%) and intergenic regions (~ 27%). We then utilized 6920 stringent selected SNPs from present study and 6714 SNPs and microsatellite markers available from previous studies for construction of linkage map. The resulting high-density linkage map comprising of eight linkage groups contained 13,590 markers which spanned 1299.14 cM of map length with an average marker density of 0.095 cM. Further, the derived linkage map was used to improve the available assembly of desi chickpea genome by anchoring 443 previously unplaced scaffolds onto eight linkage groups. The present efforts have refined anchoring of the desi chickpea genome assembly to 55.57% of the ~ 520 Mb of assembled desi genome. To the best of our knowledge, the linkage map generated in the present study represents one of the most dense linkage map developed for the crop till date. It will serve as a valuable resource for fine mapping and positional cloning of important quantitative trait loci (QTLs) associated with agronomical traits and also for anchoring and ordering of future genome sequence assemblies.

Updates on Genomic Resources in Chickpea for Crop Improvement

In recent years, rapid advancement has been done in generation of genomic resources for the important legume crop chickpea. Here, we provide an update on important advancements made on availability of genomic resources for this crop. The availability of reference genome and transcriptome sequences, and resequencing of several accessions have enabled the discovery of gene space and molecular markers in chickpea. These resources have helped in elucidating evolutionary relationship and identification of quantitative trait loci for important agronomic traits. Gene expression in different tissues/organs during development and under abiotic/biotic stresses has been interrogated. In addition, single-base resolution DNA methylation patterns in different organs have been analyzed to understand gene regulation. Overall, we provide a consolidated overview of available genomic resources of chickpea that may help in fulfilling the promises for improvement of this important crop.