Abstract
High yield has always been an essential target in almost all of the cotton breeding programs. Boll weight (BW) is a key component of cotton yield. Numerous linkage map** and genome-wide association studies (GWAS) have been performed to understand the genetic mechanism of BW, but information on the markers/genes controlling BW remains limited. In this study, we conducted a GWAS for BW using 51,268 high-quality single-nucleotide polymorphisms (SNPs) and 189 Gossypium hirsutum accessions across five different environments. A total of 55 SNPs significantly associated with BW were detected, of which 29 and 26 were distributed in the A and D subgenomes, respectively. Five SNPs were simultaneously detected in two environments. For TM5655, TM8662, TM36371, and TM50258, the BW grouped by alleles of each SNP was significantly different. The ± 550 kb regions around these four key SNPs contained 262 genes. Of them, Gh_A02G1473, Gh_A10G1765, and Gh_A02G1442 were expressed highly at 0 to 1 days post-anthesis (dpa), − 3 to 0 dpa, and − 3 to 0 dpa in ovule of TM-1, respectively. They were presumed as the candidate genes for fiber cell differentiation, initiation, or elongation based on gene annotation of their homologs. Overall, these results supplemented valuable information for dissecting the genetic architecture of BW and might help to improve cotton yield through molecular marker-assisted selection breeding and molecular design breeding.
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Data availability
The data used during this study are available from the corresponding author on reasonable request.
Abbreviations
- BW :
-
Boll weight
- SNP :
-
Single-nucleotide polymorphism
- MAS :
-
Marker-assisted selection (MAS)
- QTL :
-
Quantitative trait loci
- GWAS :
-
Genome-wide association study
- H 2 :
-
Broad-sense heritability
- MAF :
-
Minor allele frequency
- LD :
-
Linkage disequilibrium
- GAPIT :
-
Genome association and prediction integrated tool
- FarmCPU :
-
Fixed and random model circuitous probability unification
- FPKM :
-
Fragments per kilobase per million mapped read
- DPA :
-
Days post-anthesis
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Funding
This work was supported by the National Natural Science Foundation of China (32201763, 32171994), the Science and Technology Development Project of Henan Province (212102110054, 222102110146), the Key Scientific Research Projects of Higher Education of Henan Province (22A210014), the Project of Sanya Yazhou Bay Science and Technology City (SCKJ-JYRC-2022–88), and the State Key Laboratory of Cotton Biology Open Fund (CB2021A02).
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FL and QLW conceived, supervised, and managed the study. YCX, YYW, XLG, XYC, RRS, and TFQ contributed to the genotypic data. FL, ZLZ, YCX, XYC, YQH, YT, and BHL contributed to the phenotypic evaluation. YYW, XLG, RRS, TFQ, and YCX analyzed the data. YYW, XLG, RRS, and FL wrote and revised the manuscript. All authors have read and approved the final manuscript.
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Yuanyuan Wang and **nlei Guo contributed equally to this work and share the first authorship.
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Wang, Y., Guo, X., Xu, Y. et al. Genome-wide association study for boll weight in Gossypium hirsutum races. Funct Integr Genomics 23, 331 (2023). https://doi.org/10.1007/s10142-023-01261-3
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DOI: https://doi.org/10.1007/s10142-023-01261-3