Abstract
Key message
Different kinship and resistance to cotton leaf curl disease (CLCuD) and heat were found between upland cotton cultivars from China and Pakistan. 175 SNPs and 82 InDels loci related to yield, fiber quality, CLCuD, and heat resistance were identified. Elite alleles found in Pakistani accessions aided local adaptation to climatic condition of two countries.
Abstract
Adaptation of upland cotton (Gossypium hirsutum) beyond its center of origin is expected to be driven by tailoring of the genome and genes to enhance yield and quality in new ecological niches. Here, resequencing of 456 upland cotton accessions revealed two distinct kinships according to the associated country. Fiber quality and lint percentage were consistent across kinships, but resistance to cotton leaf curl disease (CLCuD) and heat was distinctly exhibited by accessions from Pakistan, illustrating highly local adaption. A total of 175 SNP and 82 InDel loci related to yield, fiber quality, CLCuD and heat resistance were identified; among them, only two overlapped between Pakistani and Chinese accessions underscoring the divergent domestication and improvement targets in each country. Loci associated with resistance alleles to leaf curl disease and high temperature were largely found in Pakistani accessions to counter these stresses prevalent in Pakistan. These results revealed that breeding activities led to the accumulation of unique alleles and helped upland cotton become adapted to the respective climatic conditions, which will contribute to elucidating the genetic mechanisms that underlie resilience traits and help develop climate-resilient cotton cultivars for use worldwide.
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Data availability
Sequences have been deposited at the National Center for Biotechnology Information (NCBI) under the accession PRJNA901674, PRJNA744011 and PRJNA752720. The genomic variants, genotype data, and phenotype data could be downloaded from http://cotton.zju.edu.cn.
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Funding
This work was supported by the National Science Foundation of China and Pakistan Science Foundation (31661143016) through a project #PSF/BSFC-AGR/P-NIBGE(12), the Leading Innovative and Entrepreneur Team Introduction Program of Zhejiang, China (2019R01002) and the Fundamental Research Funds for the Central Universities in China (226–2022-00100).
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T.Z and M.R. conceptualized the research program, designed the experiments, and coordinated the project. Z.H., Z.S., Y.H., L.H., Y.L., A.K., Y.M., S.Z. S.I., M.M., M.I., S.Z. collected the cotton samples and worked on the phenotyping. Z.H., Z.S., Y.H., and S.Z. extracted the high-quality DNA. T.Z., Z.H., Z.S. Y.H., and M.M. analyzed all the data and wrote the manuscript. All authors have read and approved the final version of the manuscript.
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Han, Z., Si, Z., Rahman, Mu. et al. Genomic insights into local adaptation of upland cotton in China and Pakistan. Theor Appl Genet 137, 136 (2024). https://doi.org/10.1007/s00122-024-04624-x
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DOI: https://doi.org/10.1007/s00122-024-04624-x