Genetic Basis of Fiber Improvement and Decreased Stress Tolerance in Cultivated Versus Semi-Domesticated Upland Cotton

Abstract

Crop domestication from wild ancestors has resulted in the wide adaptation coupled with improved yield and quality traits. However, the genetic basis of many domesticated characteristics remains to be explored. Upland cotton (Gossypium hirsutum) is the most important tetraploid cotton species, accounting for about 90% of world cotton commerce. Here, we reveal the effects of domestication on fiber and stress traits through comprehensive analyses of semi-domesticated races and cultivated cotton accessions. A total of 416 cotton accessions were genotyped, and a decrease in genetic diversity from races to landraces and modern cultivars was detected. Furthermore, 71 domestication selective sweeps (DSS) and 14 improvement selective sweeps (ISS) were identified, with the Dt sub-genome experiencing stronger selection than the At sub-genome during the both selection types. The more expressed genes and a delay in the expression peak of genes related to secondary cell wall (SCW) development in modern cultivars compared to semi-domesticated cotton races, may have contributed to long fibers in these plants. However, down-regulation of genes related to stress response was responsible for decreasing stress tolerance in modern cultivars. We further experimentally confirmed that silencing of PR1 and WRKY20, genes that showed higher expression in the semi-domesticated races, drastically compromised cotton resistance to V. dahliae. Our results reveal fiber improvement and decreased stress tolerance as a result of the domestication of modern upland cotton cultivars.

Finding Needles in a Haystack: Using Geo-References to Enhance the Selection and Utilization of Landraces in Breeding for Climate-Resilient Cultivars of Upland Cotton (Gossypium hirsutum L.)

“…Similar results were obtained from genotyping 416 accessions of varieties, wild relatives and landraces of cotton from the Chinese collection using an 80K SNP array [31]. Aside from its rich genetic diversity, landraces have also been reported to harbor novel and beneficial alleles that can be used to enhance the adaptability of cotton to various environmental pressures [31][32][33][34][35]. Research to find novel sources of genetic variation that can enhance the ability of cotton to germinate under cold conditions not only established the genetic divergence of landraces from cultivated accessions of G. hirsutum but also demonstrated their potential to germinate even under critically low temperature [32].…”

“…In particular, molecular marker profiling of a reference set composed of 1933 cultivated and wild-type accessions of G. hirsutum and G. barbadense , as well as a diverse panel of 395 Gossypium accessions from the NCGC indicated a greater genetic diversity in the landraces compared to the cultivated accessions of cotton [ 28 , 30 ]. Similar results were obtained from genotyping 416 accessions of varieties, wild relatives and landraces of cotton from the Chinese collection using an 80K SNP array [ 31 ]. Aside from its rich genetic diversity, landraces have also been reported to harbor novel and beneficial alleles that can be used to enhance the adaptability of cotton to various environmental pressures [ 31 , 32 , 33 , 34 , 35 ].…”

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

“…A kinship (K) matrix was obtained directly in the “mrMLM” program. According to our previous study [ 40 ], k = 3 was selected, and a population structure (Q) matrix was calculated by admixture version 1.3. The 52 data sets, including the phenotyping data from the different environments and the BLUP for each trait, were used for the GWAS analysis.…”

Evolutionary Origins of Drought Tolerance in Spermatophytes

“…During domestication, selection can lead to the loss of genetic diversity ( Doebley et al, 2006 ), and indirect effects of domestication may have led to the loss of particular stress tolerance traits including drought tolerance ( Yu et al, 2008 ; Zhu et al, 2019 ; Wang et al, 2020b , a ). In the same manner as drought adaptations above, domestication statuses for the same sets of plant species were assigned which were exclusively sourced from the genome paper of each plant genome.…”