Abstract
Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicerarietinum) 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.
Highlights
Germplasm sequencing efforts in some crop plants have provided insights into the global distribution of genetic variation[5]; how this diversity has been shaped by the genetic bottlenecks associated with domestication[6] and by the effects of selective breeding[7]; and, how we can link this genetic variation to phenotypic diversity[2] for breeding applications
On the basis of whole-genome sequencing (WGS) of 3,366 chickpea germplasm accessions, we report here a rich map of the genetic variation in chickpea
We propose three genomic breeding approaches— haplotype-based breeding, genomic prediction and optimal contribution selection (OCS)—for developing tailor-made high-yielding and climate-resilient chickpea varieties
Summary
Germplasm sequencing efforts in some crop plants have provided insights into the global distribution of genetic variation[5]; how this diversity has been shaped by the genetic bottlenecks associated with domestication[6] and by the effects of selective breeding[7]; and, how we can link this genetic variation to phenotypic diversity[2] for breeding applications. We developed a chickpea pan-genome (592.58 Mb) using an iterative mapping and assembly approach by combining the CDC Frontier reference genome, an additional 2.93 Mb from a desi genome (ICC 4958)12, 3.70 Mb from a Cicer reticulatum genome[13] and 53.66 Mb from de-novo-assembled sequences from cultivated (48.38 Mb; 3,171) and C. reticulatum (5.28 Mb; 28) accessions (Supplementary Data 4 Table 1). The N50 values for sequences from de-novo-assembled cultivated and C. reticulatum accessions, C. reticulatum and the desi genome were 2.61 kb, 1.30 kb, 1.78 kb and 1.76 kb, respectively, whereas the average gene length was 4.72 kb, 1.09 kb, 1.09 kb and 0.98 kb (Supplementary Data 4 Table 1) This pan-genome was further used to assess the effect of presence–absence variations on protein-coding genes (Supplementary Data 4 Table 4, Supplementary Notes)
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