Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang

Abstract

Summary Xinjiang has been the largest and highest yield cotton production region not only in China, but also in the world. Improvements in Upland cotton cultivars in Xinjiang have occurred via pedigree selection and/or crossing of elite alleles from the former Soviet Union and other cotton producing regions of China. But it is unclear how genomic constitutions from foundation parents have been selected and inherited. Here, we deep‐sequenced seven historic foundation parents, comprising four cultivars introduced from the former Soviet Union (108Ф, C1470, 611Б and KK1543) and three from United States and Africa (DPL15, STV2B and UGDM), and re‐sequenced sixty‐nine Xinjiang modern cultivars. Phylogenetic analysis of more than 2 million high‐quality single nucleotide polymorphisms allowed their classification two groups, suggesting that Xinjiang Upland cotton cultivars were not only spawned from 108Ф, C1470, 611Б and KK1543, but also had a close kinship with DPL15, STV2B and UGDM. Notably, identity‐by‐descent (IBD) tracking demonstrated that the former Soviet Union cultivars have made a huge contribution to modern cultivar improvement in Xinjiang. A total of 156 selective sweeps were identified. Among them, apoptosis‐antagonizing transcription factor gene (GhAATF1) and mitochondrial transcription termination factor family protein gene (GhmTERF1) were highly involved in the determination of lint percentage. Additionally, the auxin response factor gene (GhARF3) located in inherited IBD segments from 108Ф and 611Б was highly correlated with fibre quality. These results provide an insight into the genomics of artificial selection for improving cotton production and facilitate next‐generation precision breeding of cotton and other crops.

Comparative Dynamic Transcriptome Reveals the Delayed Secondary-Cell-Wall Thickening Results in Altered Lint Percentage and Fiber Elongation in a Chromosomal Segment Substitution Line of Cotton (Gossypium hirsutum L.)

“…Numerous candidate genes involved in regulating LP have been identified to date (Su et al, 2016 ; Han et al, 2020 ; Wang et al, 2020 ). Here, candidate genes were mined in the introgression fragment of a major QTL for LP by resequencing data and transcriptome analysis.…”

Characterization of Cotton ARF Factors and the Role of GhARF2b in Fiber Development

“…In addition, ARF2 is regulated by a variety of upstream factors at the transcription and protein levels, and participated in the pathways of auxin, gibberellin, oleoresin, ethylene and abscisic acid [30,[43][44][45]. Studies showed that G. hirsutum ARF genes promoted the trichome initiation in transgenic Arabidopsis plants [46] and was related with ber quality in cotton [47]. Further, expression of the IAA biosynthetic gene, iaaM, can signi cantly increase IAA levels in the epidermis of cotton ovules at the ber initiation stage, subsequently, increased the number of lint bers and lint percentage in a 4-year eld trial [48].…”

Inheritance, QTLs, and Candidate Genes of Lint Percentage in Upland Cotton

“…For example, 28 cotton lines with high LP (43–47%) were screened by Li and Wang (1992) , and 8 high LP (> 42%) lines were screened from former Soviet Union germplasm resources by Liu et al (1998) . Cultivars introduced from the former Soviet Union (108Ф, C1470, 611B, and KK1543), the United States, and Africa (DPL15, STV2B, and UGDM) were applied for modern cultivar improvement in Xinjiang, China ( Han et al, 2020 ). Using foreign germplasm resources, many high LP (> 43%) cultivars/lines have been bred in China.…”

“…Analysis of CSILs of SL15 (low-LP) and LMY22 (high-LP) indicate that delayed secondary-cell-wall thickening results in altered LP ( Gai et al, 2007 ). In selective sweeps, an apoptosis-antagonizing transcription factor gene ( GhAATF1 ) and mitochondrial transcription termination factor family protein gene ( GhmTERF1 ) were found to be highly involved in the determination of LP ( Han et al, 2020 ). Most of these genes are preferentially expressed at the initiation of cotton fiber and early elongation stages ( Table 3 ; Supplementary Table S5 ).…”