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A chickpea genetic variation map based on the sequencing of 3,366 genomes.

ABSTRACT: Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources¹. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level². Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

SUBMITTER: Varshney RK

PROVIDER: S-EPMC8612933 | biostudies-literature | 2021 Nov

REPOSITORIES: biostudies-literature

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A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Varshney Rajeev K RK Roorkiwal Manish M Sun Shuai S Bajaj Prasad P Chitikineni Annapurna A Thudi Mahendar M Singh Narendra P NP Du Xiao X Upadhyaya Hari D HD Khan Aamir W AW Wang Yue Y Garg Vanika V Fan Guangyi G Cowling Wallace A WA Crossa José J Gentzbittel Laurent L Voss-Fels Kai Peter KP Valluri Vinod Kumar VK Sinha Pallavi P Singh Vikas K VK Ben Cécile C Rathore Abhishek A Punna Ramu R Singh Muneendra K MK Tar'an Bunyamin B Bharadwaj Chellapilla C Yasin Mohammad M Pithia Motisagar S MS Singh Servejeet S Soren Khela Ram KR Kudapa Himabindu H Jarquín Diego D Cubry Philippe P Hickey Lee T LT Dixit Girish Prasad GP Thuillet Anne-Céline AC Hamwieh Aladdin A Kumar Shiv S Deokar Amit A AA Chaturvedi Sushil K SK Francis Aleena A Howard Réka R Chattopadhyay Debasis D Edwards David D Lyons Eric E Vigouroux Yves Y Hayes Ben J BJ von Wettberg Eric E Datta Swapan K SK Yang Huanming H Nguyen Henry T HT Wang Jian J Siddique Kadambot H M KHM Mohapatra Trilochan T Bennetzen Jeffrey L JL Xu Xun X Liu Xin X

Nature 20211110 7886

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources<sup>1</sup>. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level<sup>2</sup>. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to descri ...[more]

PMID: 34759320

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Project description:BackgroundIn the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic map using RAD-Seq (Restriction-site Associated DNA Sequencing) genotyping-by-sequencing (RAD-Seq GBS) and Illumina GoldenGate assays, and to examine the alignment of the current map with the kabuli chickpea genome assembly.ResultsGenic single nucleotide polymorphisms (SNPs) totaling 51,632 SNPs were identified by 454 transcriptome sequencing of Cicer arietinum and Cicer reticulatum genotypes. Subsequently, an Illumina GoldenGate assay for 1,536 SNPs was developed. A total of 1,519 SNPs were successfully assayed across 92 recombinant inbred lines (RILs), of which 761 SNPs were polymorphic between the two parents. In addition, the next generation sequencing (NGS)-based GBS was applied to the same population generating 29,464 high quality SNPs. These SNPs were clustered into 626 recombination bins based on common segregation patterns. Data from the two approaches were used for the construction of a genetic map using a population derived from an intraspecific cross. The map consisted of 1,336 SNPs including 604 RAD recombination bins and 732 SNPs from Illumina GoldenGate assay. The map covered 653 cM of the chickpea genome with an average distance between adjacent markers of 0.5 cM. To date, this is the most extensive genetic map of chickpea using an intraspecific population. The alignment of the map with the CDC Frontier genome assembly revealed an overall conserved marker order; however, a few local inconsistencies within the Cicer arietinum pseudochromosome 1 (Ca1), Ca5 and Ca8 were detected. The map enabled the alignment of 215 unplaced scaffolds from the CDC Frontier draft genome assembly. The alignment also revealed varying degrees of recombination rates and hotspots across the chickpea genome.ConclusionsA high-density genetic map using RAD-Seq GBS and Illumina GoldenGate assay was developed and aligned with the existing kabuli chickpea draft genome sequence. The analysis revealed an overall conserved marker order, although some localized inversions between draft genome assembly and the genetic map were detected. The current analysis provides an insight of the recombination rates and hotspots across the chickpea genome.

Dataset Information

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Publications

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

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