Identification of QTNs and Their Candidate Genes for Boll Number and Boll Weight in Upland Cotton

Author:

Shi Xiaoshi1,Feng Changhui2,Qin Hongde2,Wang Jingtian1ORCID,Zhao Qiong1,Jiao Chunhai3,Zhang Yuanming1ORCID

Affiliation:

1. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China

2. Institute of Industrual Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China

3. Hubei Academy of Agricultural Sciences, Wuhan 430064, China

Abstract

Genome-wide association study (GWAS) has identified numerous significant loci for boll number (BN) and boll weight (BW), which play an essential role in cotton (Gossypium spp.) yield. The North Carolina design II (NC II) genetic mating population exhibits a greater number of genetic variations than other populations, which may facilitate the identification of additional genes. Accordingly, the 3VmrMLM method was employed for the analysis of upland cotton (Gossypium hirsutum L.) in an incomplete NC II genetic mating population across three environments. A total of 204 quantitative trait nucleotides (QTNs) were identified, of which 25 (24.75%) BN and 30 (29.13%) BW QTNs were of small effect (<1%) and 24 (23.76%) BN and 20 (19.42%) BW QTNs were rare (<10%). In the vicinity of these QTNs, two BN-related genes and two BW-related genes reported in previous studies were identified, in addition to five BN candidate genes and six BW candidate genes, which were obtained using differential expression analysis, gene function annotation, and haplotype analysis. Among these, six candidate genes were identified as homologs of Arabidopsis genes. The present study addresses the limitation of heritability missing and uncovers several new candidate genes. The findings of this study can provide a basis for further research and marker-assisted selection in upland cotton.

Funder

National Natural Science Foundation of China

Publisher

MDPI AG

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