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Theoretical and Applied Genetics

, Volume 132, Issue 4, pp 989–999 | Cite as

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

  • Gregory N. Thyssen
  • Johnie N. Jenkins
  • Jack C. McCarty
  • Linghe Zeng
  • B. Todd Campbell
  • Christopher D. Delhom
  • Md. Sariful Islam
  • Ping Li
  • Don C. Jones
  • Brian D. Condon
  • David D. FangEmail author
Original Article

Abstract

Key message

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.

Notes

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.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Availability of data and materials

All relevant data reported in this paper are within the paper and its online supplementary files.

Supplementary material

122_2018_3254_MOESM1_ESM.tif (1.8 mb)
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)
122_2018_3254_MOESM2_ESM.pdf (13.7 mb)
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)
122_2018_3254_MOESM3_ESM.tif (197 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)
122_2018_3254_MOESM4_ESM.xlsx (3.2 mb)
Supplementary material 4 (XLSX 3229 kb)

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Copyright information

© This is a U.S. government work and its text is not subject to copyright protection in the United States; however, its text may be subject to foreign copyright protection 2018

Authors and Affiliations

  • Gregory N. Thyssen
    • 1
    • 2
  • Johnie N. Jenkins
    • 3
  • Jack C. McCarty
    • 3
  • Linghe Zeng
    • 4
  • B. Todd Campbell
    • 5
  • Christopher D. Delhom
    • 6
  • Md. Sariful Islam
    • 7
  • Ping Li
    • 1
  • Don C. Jones
    • 8
  • Brian D. Condon
    • 2
  • David D. Fang
    • 1
    Email author
  1. 1.Cotton Fiber Bioscience Research UnitUSDA-ARS-SRRCNew OrleansUSA
  2. 2.Cotton Chemistry and Utilization UnitUSDA-ARS-SRRCNew OrleansUSA
  3. 3.Genetics and Sustainable Agriculture Research UnitUSDA-ARSMississippi StateUSA
  4. 4.Crop Genetics Research UnitUSDA-ARSStonevilleUSA
  5. 5.Coastal Plain Soil, Water and Plant Conservation Research UnitUSDA-ARSFlorenceUSA
  6. 6.Cotton Structure and Quality Research UnitUSDA-ARS-SRRCNew OrleansUSA
  7. 7.Sugarcane Production Research UnitUSDA-ARSCanal PointUSA
  8. 8.Cotton IncorporatedCaryUSA

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