Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

Plant Biotechnology Journal
Xiongfeng MaDaigang Yang

Abstract

Upland cotton (Gossypium hirsutum) is the world's largest source of natural fibre and dominates the global textile industry. Hybrid cotton varieties exhibit strong heterosis that confers high fibre yields, yet the genome-wide effects of artificial selection that have influenced Upland cotton during its breeding history are poorly understood. Here, we resequenced Upland cotton genomes and constructed a variation map of an intact breeding pedigree comprising seven elite and 19 backbone parents. Compared to wild accessions, the 26 pedigree accessions underwent strong artificial selection during domestication that has resulted in reduced genetic diversity but stronger linkage disequilibrium and higher extents of selective sweeps. In contrast to the backbone parents, the elite parents have acquired significantly improved agronomic traits, with an especially pronounced increase in the lint percentage. Notably, identify by descent (IBD) tracking revealed that the elite parents inherited abundant beneficial trait segments and loci from the backbone parents and our combined analyses led to the identification of a core genomic segment which was inherited in the elite lines from the parents Zhong 7263 and Ejing 1 and that was strongly ass...Continue Reading

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Methods Mentioned

BETA
genotyping
dissection
Illumina sequencing
electrophoresis
PCR
PCA

Software Mentioned

R scripts
BWA ( Burrows Wheeler Aligner
plink
PHYLIP
EXCEL
TASSEL
SAMtools

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