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Genome-wide association study reveals novel genes on different chromosomal positions regulating boll weight in upland cotton (Gossypium hirsutum L.)

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Abstract

The boll weight (BW) is the most decisive yield component character and is utilized as a key index for selection in various cotton improvement programs. In the current study, 1260 accessions of cotton with a diverse genetic background were assessed for boll weight across four different environments (two locations for each environment) in China. A genome-wide association study (GWAS) was performed to mine novel single nucleotide polymorphisms (SNPs) controlling boll weight characteristics. A total of 1,122,352 SNPs were identified in association with boll weight across multiple environments, of which 138 were designated as key SNPs, harboring significantly higher association peaks for the all chromosomes on the basis of log10 P value (− log10 ≥ 6). Among 53 significant associations related to BW development across environments were identified. Six genes in the vicinity of these key SNPs (Pentatricopeptide repeat-containing protein PCMP-E76), Trihelix transcription factor ASIL2, Auxin-responsive protein SAUR50, Floral homeotic protein AGAMOUS (AG), Piriformospora indica-insensitive protein 2 (PII-2), and LOB domain-containing protein 16 (LBD16) exhibited higher expression patterns. These identified BW-related key SNPs and candidate genes could prove to have potential for influencing BW development in upland cotton. The outcome of the current study will serve as a base for further mechanistic research focused on the exploitation of BW for accelerated cotton improvement.

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Abbreviations

AY:

Henan-Anyang

BLUP:

Best linear unbiased prediction

BW:

Boll weight

Chr:

Chromosome

CS:

Hunan-Changsha

EMMAX:

Efficient mixed-model association expedited

Gh:

Gossipium Hirsutum L.

GWAS:

Genome wide association study

JS:

JiangSu

LD:

Linkage disequilibrium

Pop:

Population

SJZ:

Hebei-Shijiazhuang

SNPs:

Single nucleotide polymorphisms

TPM:

Transcripts per million

XJ1:

XinJiang-Urumchi

XJ2:

XinJiang-Alaer

XJ3:

Xinjiang-Shihezi

XJ4:

XinJiang-Shihezi

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Acknowledgements

The authors extend their appreciation to the Researchers Supporting Project number (RSP-2024R241), King Saud University, Riyadh, Saudi Arabia. Moreover, authors are thankful to Institute of Cotton Research, Chinese Academy of Agricultural Sciences for providing research related facilities to carry out present investigation.

Funding

No specific funding has been received to carry out present research work.

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Authors and Affiliations

  1. Institute of Cotton Research, Chinese Academy of Agricultural Sciences, State Key Laboratory of Cotton Biology, Anyang, 455000, Henan, People’s Republic of China

    Zubair Iqbal, Muhammad Shahid Iqbal, Zareen Sarfraz, Mian Faisal Nazir, Daowu Hu, Muhammad Mubashar Zafar,  Shoupuhe, Tahir Mahmood, Zhaoe Pan & Xiongming Du

  2. Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia

    Salman Alamery & Kotb A. Attia

  3. Department of Plant Breeding and Genetics, The University of Haripur, Haripur, 22620, Pakistan

    Khurram Shehzad & Sajid Fiaz

  4. Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, 572025, People’s Republic of China

    Qamar U. Zaman

  5. College of Tropical Crops, Hainan University, Haikou, 570228, People’s Republic of China

    Qamar U. Zaman

  6. Institute of Biotechnology and Genetic Engineering, The University of Agriculture, Peshawar, Pakistan

    Safira Attacha

  7. State Key Laboratory of Rice Biology/Key Laboratory of Rice Biology and Breeding, Ministry of Agriculture/China National Rice Research Institute, Hangzhou, 310006, People’s Republic of China

    Aqib Zeb

  8. Department of Botany, Hazara University, Mansehra, Pakistan

    Alia Gul

  9. Biotechnology School, Nile University, 26th of July Corridor, Sheikh Zayed City, 12588, Giza, Egypt

    Asmaa M. Abushady

  10. Department of Genetics, Agriculture College, Ain Shams University, Cairo, Egypt

    Asmaa M. Abushady

  11. Institute of Science and Technology, Niigata University, Ikarashi-2, Nishi-ku, Niigata, 950-2181, Japan

    Itoh Kimiko

Authors
  1. Zubair Iqbal
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  2. Muhammad Shahid Iqbal
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  3. Salman Alamery
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  4. Khurram Shehzad
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  5. Qamar U. Zaman
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  6. Safira Attacha
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  8. Mian Faisal Nazir
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  9. Daowu Hu
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  10. Muhammad Mubashar Zafar
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  11. Aqib Zeb
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  12. Shoupuhe
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  13. Tahir Mahmood
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  14. Sajid Fiaz
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  15. Alia Gul
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  16. Asmaa M. Abushady
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  17. Itoh Kimiko
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  18. Kotb A. Attia
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  19. Zhaoe Pan
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  20. Xiongming Du
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Contributions

XD and ZP designed the study, ZI, MSI, ZS conducted research, MFN, DH, MZ, S and TM helped ZI to perform the experiments and data collection. QUZ, AZ, MSI, ZP, DH and TM helped in data analysis, software standardization and writing of original draft. SF, SA, IK, AMA, SA and KAA provided technical expertise to improve the article and helped in funding acquisition. All authors review and edited the manuscript.

Corresponding authors

Correspondence to Sajid Fiaz or Xiongming Du.

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Iqbal, Z., Iqbal, M.S., Alamery, S. et al. Genome-wide association study reveals novel genes on different chromosomal positions regulating boll weight in upland cotton (Gossypium hirsutum L.). Genet Resour Crop Evol 71, 785–799 (2024). https://doi.org/10.1007/s10722-023-01657-x

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