Genome-Wide SNP Discovery and Mapping QTLs for Seed Iron and Zinc Concentrations in Chickpea (Cicer arietinum L.)

Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea (Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2 : 3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F2 : 3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7%(CaqZn8.1) and 13.7%(CaqZn4.3). Three QTLs for seed Fe and Zn concentrations (CaqFe4.4, CaqFe4.5, and CaqZn4.1) were colocated in the “QTL-hotspot” region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties

Two decades of association mapping: Insights on disease resistance in major crops

Climate change across the globe has an impact on the occurrence, prevalence, and severity of plant diseases. About 30% of yield losses in major crops are due to plant diseases; emerging diseases are likely to worsen the sustainable production in the coming years. Plant diseases have led to increased hunger and mass migration of human populations in the past, thus a serious threat to global food security. Equipping the modern varieties/hybrids with enhanced genetic resistance is the most economic, sustainable and environmentally friendly solution. Plant geneticists have done tremendous work in identifying stable resistance in primary genepools and many times other than primary genepools to breed resistant varieties in different major crops. Over the last two decades, the availability of crop and pathogen genomes due to advances in next generation sequencing technologies improved our understanding of trait genetics using different approaches. Genome-wide association studies have been effectively used to identify candidate genes and map loci associated with different diseases in crop plants. In this review, we highlight successful examples for the discovery of resistance genes to many important diseases. In addition, major developments in association studies, statistical models and bioinformatic tools that improve the power, resolution and the efficiency of identifying marker-trait associations. Overall this review provides comprehensive insights into the two decades of advances in GWAS studies and discusses the challenges and opportunities this research area provides for breeding resistant varieties

Meta-QTL analysis enabled identification of candidate genes and haplotypes for enhancing biotic stress resistance in chickpea

Fusarium wilt, Ascochyta blight and Botrytis grey mould caused by fungal pathogens are major biotic stresses that lead to 100% yield loss in chickpea (Cicer arietinum L.). Several independent studies reported the genomic regions, using heterogeneous populations, that are of limited use in breeding programs for the development of enhanced disease resistance in climate change scenarios. In order to identify the consensus genomic regions, we developed a consensus integrated map and performed Meta-QTL analysis using 52 QTLs reported in 17 independent studies. The consensus integrated map spanned 1292.04 cM with 669 markers on all eight linkage groups. In total, we report 10 Meta-QTLs distributed on four linkage groups (CaLG02, CaLG03, CaLG04 and CaLG06) and 172 genes belonging to a wide range of gene-families that are involved in multiple disease resistance. Among these, the key genes such as Glutaredoxin, Reticuline oxidase-like protein, and RING-Finger proteins, which have been previously reported for disease resistance. The confidence interval of reported Meta-QTLs decreased 4.89 folds from the original QTL studies whose confidence interval ranged from 0.84 to 28.94 cM. Among these genes, Ca_13066 and Ca_05186 present in Meta-QTL4_6 and Meta-QTL6_8, that play major role in biotic stress resistance pathways possessed 3 and 8 haplotypes respectively. Our study provides a better understanding of the genetic mechanisms underlying these three important biotic stresses. Further, the Meta-QTLs, candidate genes and haplotypes reported in this study can be used for developing climate resilient and disease resistant chickpea cultivars

Genome-Wide SNP discovery and mapping QTLs for seed iron and zinc concentrations in Chickpea (Cicer arietinum L.)

Biofortification through plant breeding is a cost-effective and sustainable approach towards addressing micronutrient malnutrition prevailing across the globe. Screening cultivars for micronutrient content and identification of quantitative trait loci (QTLs)/genes and markers help in the development of biofortified varieties in chickpea (Cicer arietinum L.). With the aim of identifying the genomic regions controlling seed Fe and Zn concentrations, the F2:3 population derived from a cross between MNK-1 and Annigeri 1 was genotyped using genotyping by sequencing approach and evaluated for Fe and Zn concentration. An intraspecific genetic linkage map comprising 839 single nucleotide polymorphisms (SNPs) spanning a total distance of 1,088.04 cM with an average marker density of 1.30 cM was constructed. By integrating the linkage map data with the phenotypic data of the F2:3 population, a total of 11 QTLs were detected for seed Fe concentration on CaLG03, CaLG04, and CaLG05, with phenotypic variation explained ranging from 7.2% (CaqFe3.4) to 13.4% (CaqFe4.2). For seed Zn concentration, eight QTLs were identified on CaLG04, CaLG05, and CaLG08. The QTLs individually explained phenotypic variations ranging between 5.7% (CaqZn8.1) and 13.7% (CaqZn4.3). Three QTLs for seed Fe and Zn concentrations (CaqFe4.4, CaqFe4.5, and CaqZn4.1) were colocated in the “QTL-hotspot” region on CaLG04 that harbors several drought tolerance-related QTLs. We identified genes in the QTL regions that encode iron–sulfur metabolism and zinc-dependent alcohol dehydrogenase activity on CaLG03, iron ion binding oxidoreductase on CaLG04, and zinc-induced facilitator-like protein and ZIP zinc/iron transport family protein on CaLG05. These genomic regions and the associated markers can be used in marker-assisted selection to increase seed Fe and Zn concentrations in agronomically superior chickpea varieties

Translational Chickpea Genomics Consortium to accelerate genetic gains in chickpea (Cicer arietinum L.)

The Translational Chickpea Genomics Consortium (TCGC) was set up to increase the production and productivity of chickpea (Cicer arietinum L.). It represents research institutes from six major chickpea growing states (Madhya Pradesh, Maharashtra, Andhra Pradesh, Telangana, Karnataka and Uttar Pradesh) of India. The TCGC team has been engaged in deploying modern genomics approaches in breeding and popularizing improved varieties in farmers’ fields across the states. Using marker-assisted backcrossing, introgression lines with enhanced drought tolerance and fusarium wilt resistance have been developed in the genetic background of 10 elite varieties of chickpea. Multi-location evaluation of 100 improved lines (70 desi and 30 kabuli) during 2016–2017 and 2018–2019 enabled the identification of top performing desi and kabuli lines. In total, 909 Farmer Participatory Varietal Selection trials were conducted in 158 villages in 16 districts of the five states, during 2017–2018, 2018–2019, and 2019–2020, involving 16 improved varieties. New molecular breeding lines developed in different genetic backgrounds are potential candidates for national trials under the ICAR-All India Coordinated Research Project on Chickpea. The comprehensive efforts of TCGC resulted in the development and adoption of high-yielding varieties that will increase chickpea productivity and the profitability of chickpea growing farmers

A Scintillating Journey of Genomics in Simplifying Complex Traits and Development of Abiotic Stress Resilient Chickpeas

Chickpea (Cicer arietinum L.) is an important cool season food legume cultivated in more than 55 countries across the globe. In the context of climate change, productivity of chickpea is hampered by higher incidence of abiotic and biotic stresses. Among abiotic stresses, drought, heat, cold and salinity are the most important yield limiting factors. Advanced genomics technologies have great potential to accelerate mapping, gene discovery, marker development and genomics-assisted breeding. Integration of precise phenotypic data along with sequence information will help in developing cultivars tolerant to various abiotic stresses. In this chapter, we discuss the impact of various abiotic stresses on chickpea production and provide an update on potential strategies to develop stress-tolerant chickpea cultivars. In addition, we also summarize the systematic efforts of simplifying the complex traits in chickpea as well as development of improved varieties with tolerance to abiotic stresses during last decade. In addition, we also highlight the emerging stresses and future strategies to combat the abiotic stresses