A GWAS identified loci and candidate genes associated with fiber quality traits in a new cotton MAGIC population.

Publisher: Springer Country of Publication: Germany NLM ID: 0145600 Publication Model: Electronic Cited Medium: Internet ISSN: 1432-2242 (Electronic) Linking ISSN: 00405752 NLM ISO Abbreviation: Theor Appl Genet Subsets: MEDLINE

Original Publication: Berlin, New York, Springer

Gossypium*/genetics ; Gossypium*/growth & development ; Cotton Fiber*/analysis ; Quantitative Trait Loci* ; Polymorphism, Single Nucleotide* ; Phenotype*; Genotype ; Genetic Association Studies ; Chromosome Mapping/methods ; Plant Breeding ; Genes, Plant ; Crosses, Genetic ; Alleles ; Tetraploidy ; Genome-Wide Association Study

Key Message: GWAS of a new MAGIC population containing alleles from five tetraploid Gossypium species identified novel fiber QTL and confirmed previously identified stable QTL. Identification of loci and underlying genes for fiber quality traits will facilitate genetic improvement in cotton fiber quality. In this research, a genome-wide association study (GWAS) was carried out for fiber quality attributes using a new multi-parent advanced generation inter-cross (MAGIC) population consisting of 372 recombinant inbred lines (RILs). Sixteen parents including 12 exotic germplasm lines derived from five tetraploid Gossypium species and 4 Upland cotton varieties were intercrossed to develop the population. Both RILs and parental lines were evaluated at three locations, College Station, Texas; Las Cruses, New Mexico; and Stoneville, Mississippi, from 2016 through 2023. Fiber length (UHM) had positive correlation with strength (STR) and length uniformity (UNI) and a negative correlation with micronaire (MIC) and elongation (ELO). By combining all the data from all locations, we identified significant SNPs for ELO, UHM, and UNI while STR and MIC were location dependent. These results suggest an important role of genotype by environment interaction in a GWAS of fiber traits. Twenty possible novel fiber QTL were identified: 10 for STR, three for UNI, and seven for MIC. The QTL for ELO (Chr.D04: 53-Mb), UHM (Chr.D11: 24-Mb), and UNI (Chr.D04: 34-Mb) were stable across multiple environments and may be useful for marker-assisted selection to improve fiber quality. For STR, we found candidate genes Gh_A07G1574 and Gh_A07G1581 to be present in the previously identified QTL region (Chr.A07: 77-Mb) on chromosome A07. Identified loci and their corresponding candidate genes will be useful to improve fiber quality via marker-assisted selection in a cotton breeding.
Competing Interests: Declarations. Conflict of interest: The authors declare that they have no conflict of interest.
(© 2024. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

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6054-21000-019-00D Agricultural Research Service; 6066-21000-052-00D Agricultural Research Service

Date Created: 20241223 Date Completed: 20241223 Latest Revision: 20241223

20241223

10.1007/s00122-024-04800-z

39714714