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 (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.

Breeding custom‐designed crops for improved drought adaptation

“…The integration of gene bank passport data and weather data from the target population of environments (TPE) can be utilized to identify superior haplotypes for specific adaptive traits, which could be used in haplotype-based breeding (discussed below). 11 Additionally, deleterious alleles (genetic load) associated with the trait(s) of interest could be identified by utilizing genomic evolution parameters and amino acid conservation modeling, as demonstrated in cassava 67 and chickpea, 66 and eliminated using molecular breeding or genome editing strategies. 68 As a result, superior parental lines…”

Comparative Flower Transcriptome Network Analysis Reveals DEGs Involved in Chickpea Reproductive Success during Salinity

“…Additionally, chickpea has a narrow genetic base. It shows phenotypic plasticity, making it challenging to underpin the physiological responses and uncover the genes responsible for flower development during salt stress [ 20 , 21 ]. It is essential to understand the transcriptome dynamics and elucidate the molecular mechanisms in response to salt tolerance to unravel the phenotypic plasticity barriers.…”

Expanding Gene-Editing Potential in Crop Improvement with Pangenomes

“…Due to falling sequencing costs and the increased acknowledgment of significant gene presence/absence variation in some species, pangenomes have expanded beyond bacteria to higher organisms such as chicken [44] and human [45] as well as many plant species, allowing the analysis of the large-scale PAV observed in plants [46,47]. Pangenomics in plants was first proposed by Morgante et al in 2007 [48] and since then, pangenomes have been assembled for many crop plant species including soybean (Glycine max) [49,50], maize (Zea mays) [51], tomato (Solanum lycopersicum) [35], Brassica oleracea [39], Brassica napus [27,52], Brachypodium distachyon [53], barley (Hordeum vulgare) [54], rice [55], pigeon pea (Cajanus cajan) [29,56], apple (Malus domestica) [57], capsicum [25], sesame (Sesamum indicum) [58], sunflower (Helianthus annuus) [59], yuca (Manihot esculenta) [60], sorghum (Sorghum bicolor) [36,61], and bread wheat (Triticum aestivum) [62]. Pangenomes for non-food plant species such as Arabidopsis thaliana [63], Amborella trichopoda [64], cotton (Gossypium) [65], and barrel clover (Medicago truncatula) [66] have also been published (Table 1).…”