Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton ( Go
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ORIGINAL ARTICLE
Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum) Panhong Dai1,3 · Gaofei Sun1,4 · Yinhua Jia1 · Zhaoe Pan1 · Yingbing Tian3 · Zhen Peng1,2 · Hongge Li1,2 · Shoupu He1,2 · Xiongming Du1,2 Received: 28 February 2020 / Accepted: 8 August 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Abstract Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding. Keywords Population divergence · Upland cotton · Chromosome inversion · Genome-wide association study (GWAS) · Environmental adaptability
Introduction Communicated by Mikko J. Sillanpaa. Panhong Dai and Gaofei Sun have contributed equally. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03668-z) contains supplementary material, which is available to authorized users. * Shoupu He [email protected] * Xiongming Du [email protected] Extended author information available on the last page of the article
Protecting plant populations against the harmful effects of climate change is one of the most important goals of plant genetic research
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