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Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.)

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Significant associations between candidate genes and six major cotton fiber quality traits were identified in a MAGIC population using GWAS and whole genome sequencing.

Abstract

Upland cotton (Gossypium hirsutum L.) is the world’s major renewable source of fibers for textiles. To identify causative genetic variants that influence the major agronomic measures of cotton fiber quality, which are used to set discount or premium prices on each bale of cotton in the USA, we measured six fiber phenotypes from twelve environments, across three locations and 7 years. Our 550 recombinant inbred lines were derived from a multi-parent advanced generation intercross population and were whole-genome-sequenced at 3× coverage, along with the eleven parental cultivars at 20× coverage. The segregation of 473,517 single nucleotide polymorphisms (SNPs) in this population, including 7506 non-synonymous mutations, was combined with phenotypic data to identify seven highly significant fiber quality loci. At these loci, we found fourteen genes with non-synonymous SNPs. Among these loci, some had simple additive effects, while others were only important in a subset of the population. We observed additive effects for elongation and micronaire, when the three most significant loci for each trait were examined. In an informative subset where the major multi-trait locus on chromosome A07:72-Mb was fixed, we unmasked the identity of another significant fiber strength locus in gene Gh_D13G1792 on chromosome D13. The micronaire phenotype only revealed one highly significant genetic locus at one environmental location, demonstrating a significant genetic by environment component. These loci and candidate causative variant alleles will be useful to cotton breeders for marker-assisted selection with minimal linkage drag and potential biotechnological applications.

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Acknowledgements

This research was funded mainly by the USDA Agricultural Research Service CRIS Projects 6054-21000-017-00D (GNT, DDF), 6064-21000-016-00D (JNJ, JCM), 6066-21000-051-00D (LZ), and 6082-21000-008-00D (BTC). Additional funding was provided by Cotton Incorporated Projects 10-747 and 15-751 awarded to DDF, and Project 09-541 to JNJ. Mention of trade names or commercial products in this article is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the USDA which is an equal opportunity provider and employer.

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Authors and Affiliations

  1. Cotton Fiber Bioscience Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA

    Gregory N. Thyssen, Ping Li & David D. Fang

  2. Cotton Chemistry and Utilization Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA

    Gregory N. Thyssen & Brian D. Condon

  3. Genetics and Sustainable Agriculture Research Unit, USDA-ARS, Mississippi State, MS, 39762, USA

    Johnie N. Jenkins & Jack C. McCarty

  4. Crop Genetics Research Unit, USDA-ARS, Stoneville, MS, 38776, USA

    Linghe Zeng

  5. Coastal Plain Soil, Water and Plant Conservation Research Unit, USDA-ARS, Florence, SC, 29501, USA

    B. Todd Campbell

  6. Cotton Structure and Quality Research Unit, USDA-ARS-SRRC, New Orleans, LA, 70124, USA

    Christopher D. Delhom

  7. Sugarcane Production Research Unit, USDA-ARS, Canal Point, FL, 33438, USA

    Md. Sariful Islam

  8. Cotton Incorporated, Cary, NC, 27513, USA

    Don C. Jones

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  1. Gregory N. Thyssen
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Correspondence to David D. Fang.

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Communicated by Yunbi Xu.

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Fig. S1.

VanRaden kinship matrix of 550 RILs in the MAGIC population. Color key and histogram of values is shown at top left (TIFF 1817 kb)

Fig. S2.

GWAS Manhattan plots for each of six traits at each of twelve location-years. Chromosomes are labeled 1–13 for Chr. A01–A13, and 14–26 for D01–D13. Location and trait abbreviations: Stoneville, MS, USA (STV), Starkville, MS, USA (MSU), Florence, SC, USA (FLO), elongation (ELO), micronaire (MIC), short fiber index (SFI), fiber strength (STR), upper half mean length (UHML), and uniformity index (UI) (PDF 14026 kb)

Fig. S3.

Violin plot of MIC values for RILs based on genotypes at the three loci discussed in the text. Genotypes are presented along the horizontal axis, with the high-MIC haplotype indicated with a dark gray rectangle and the low-MIC haplotypes with a light gray rectangle. The number (N) of RILs in each group is indicated. See also Fig. 6. For pairwise t test p values see Table S10 (TIFF 197 kb)

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Thyssen, G.N., Jenkins, J.N., McCarty, J.C. et al. Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.). Theor Appl Genet 132, 989–999 (2019). https://doi.org/10.1007/s00122-018-3254-8

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