Whole genome resequencing and phenotyping of MAGIC population for high resolution mapping of drought tolerance in chickpea

Abstract

Terminal drought is one of the major constraints to crop production in chickpea (Cicer arietinum L.). In order to map drought tolerance related traits at high resolution, we sequenced multi‐parent advanced generation intercross (MAGIC) population using whole genome resequencing approach and phenotyped it under drought stress environments for two consecutive years (2013–14 and 2014–15). A total of 52.02 billion clean reads containing 4.67 TB clean data were generated on the 1136 MAGIC lines and eight parental lines. Alignment of clean data on to the reference genome enabled identification of a total, 932,172 of SNPs, 35,973 insertions, and 35,726 deletions among the parental lines. A high‐density genetic map was constructed using 57,180 SNPs spanning a map distance of 1606.69 cM. Using compressed mixed linear model, genome‐wide association study (GWAS) enabled us to identify 737 markers significantly associated with days to 50% flowering, days to maturity, plant height, 100 seed weight, biomass, and harvest index. In addition to the GWAS approach, an identity‐by‐descent (IBD)‐based mixed model approach was used to map quantitative trait loci (QTLs). The IBD‐based mixed model approach detected major QTLs that were comparable to those from the GWAS analysis as well as some exclusive QTLs with smaller effects. The candidate genes like FRIGIDA and CaTIFY4b can be used for enhancing drought tolerance in chickpea. The genomic resources, genetic map, marker‐trait associations, and QTLs identified in the study are valuable resources for the chickpea community for developing climate resilient chickpeas.

Exploring the genomics of abiotic stress tolerance and crop resilience to climate change

“…In recent years, specialized mapping populations involving the crossing of multiple parental lines, for example, the multi-parent advanced generation intercross (MAGIC) (Cavanagh et al, 2008), have been employed to genetically dissect complex traits. In this special section, Thudi et al (2023) utilized the desi chickpea MAGIC population for fine mapping of drought tolerance in chickpeas. GWAS identified 737 markers significantly linked to crucial agronomic traits, including days to 50% flowering, days to maturity, biomass, and 100-seed weight, among others.…”

Bioinformatics for Plant Genetics and Breeding Research

“…Ever since the rediscovery of Mendelian laws, there has been a paradigm shift in understanding the phenotype-based trait genetics to the use of molecular markers, genomics, genomes and sequence-based trait dissection (Varshney et al 2019;Thudi et al 2023). During the last two decades, genomics and NGS (next-generation sequencing) technologies have not only revolutionized our understanding of molecular basis of economically important traits, but also increased the rate of adoption of modern breeding approaches to develop climate-resilient crop varieties (Thudi et al 2020;Varshney et al 2021a).…”

Fourier-Transform Mid-Infrared (FT-MIR) Spectroscopy as a High-Throughput Phenotyping Tool for Measuring Total Fatty Acids in Chickpea (Cicer arietinum L.) Flour

“…Chickpea (Cicer arietinum L.) is the second-most cultivated pulse crop worldwide, with 15.8 million tons produced across 57 countries in 2021. , Chickpea contains 50–58% carbohydrates, 15–22% protein, 4–10% fat, and a range of minerals and vitamins (i.e., K, Mg, Ca, Zn, vitamins A, C, E, etc. ). − Compared to other pulses, the fat content in chickpeas is high .…”