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Nature Genetics Published Article from HZAU on Cotton Domestication

On March 7th, 2017, Nature Genetics online published an article of the cotton team led by Professor Zhang Xianlong from HZAU titled Asymmetric subgenome selection and cis-regulatory in the process of domestication of cotton Divergence during cotton domestication. This study not only presents the genetic basis of cotton fiber domestication for the first time, but also illustrates the effect of domestication on gene transcription regulation. The result is a new significant progress in the field of cotton genome, which provides new insights into the cotton functional genomics research and genetic improvement. Both Prof. Zhang Xianlong from HZAU and Professor Keith Lindsey from University of Durham are the corresponding authors; the doctoral student Wang Maojun from HZAU is the first author.

Cotton fiber is such an important natural textile fiber that plays an important role in the national economy. Cotton cultivars for production are mostly allotetraploid upland cotton (Gossypium hirsutum) due to its wide ecological adaptability and high fiber production accounting for more than 95% of annual cotton output. Cotton has occurred over more than 5000 years of domestication. Among many genetic variations in wild cotton accessions, some excellent ones have been selected through long-term domestication, thus significantly changing the main agronomic traits of upland cotton. And yet, very little research has addressed the genetic basis of these traits.

China began to cultivate upland cotton in the early 20th century mainly through introduction from the United States. However, genetic breeding hit the wall as a result of narrow genetic resources and high homogeneity in China. In order to unravel the effect of domestication on the genome, the researchers collected 31 wild cotton accessions and 321 domesticated cotton accessions from main cotton growing regions around the world for genome re-sequencing. The researchers, using these data, described the first comprehensive variation map of upland cotton, including single nucleotide polymorphism (SNP), insertion/deletion (In Del) and structural variation (SV). The researchers identified 93 domestication sweeps by comparing wild cotton accessions with domesticated ones through genome-wide study. These domestication sweeps contain a large number of functional genes, which are related to some major agronomic traits of upland cotton such as plant height, disease resistance and fiber quality. In the future, these domestication sweeps can be integrated by means of molecular breeding so that wild cotton accessions can be used to improve the main agronomic traits of cotton.

The long-term domestication significantly improved the yield and quality of the fiber of upland cotton. Domesticated cotton accessions enjoy a higher yield and better quality than wild ones. Domesticated cotton accessions can produce white fiber, while the wild cotton accessions can only produce fiber with light brownish yellow. In order to explore the genetic basis for controlling these traits, the research team at first used 267 materials to identify 19 candidate loci for fiber-quality-related traits through a genome-wide association study, among which 4 loci were located in the domestication sweeps. The team further identified some genes respectively selected from the A sub-genome and D sub-genome of upland cotton, the former of which was associated with the length of the fiber, and the latter with stress responses. These genes, down-regulated in the domesticated cotton accessions, are conducive to elongation of fiber and growth of white fiber. Having a knowledge of these important genetic loci of controlling fiber quality traits enabled researchers to further improve the quality of cotton fiber.

The expression levels of a large number of genes tend to be changed during the process of crops domestication. In order to analyze the causes of gene differential expression, the researchers combined digestion and sequencing of Type I Enzymes DNA with three-dimensional genome technology to identify a large number of cis-regulatory elements on the promoters and long-distance enhancer elements. These transcriptional regulatory elements were strongly acclimatized with relation to gene differential expression. This study is the first time to analyze the regulatory variation in the non-coding sweeps of plants, which provides an important reference to the exploration of functional variation in other species.

(By Li Yumei)