Genetic Detection of Lint Percentage Applying Single-Locus and Multi-Locus Genome-Wide Association Studies in Chinese Early-Maturity Upland Cotton.

Junji Su,Fushun Hao,Qi Ma,Xinzhu Ning,Jilian Li,Caixiang Wang,Ji Wang

doi:10.3389/fpls.2019.00964

Abstract

Upland cotton (Gossypium hirsutum L.) is the most important source of natural fiber in the world. Early-maturity upland cotton varieties are commonly planted in China. Nevertheless, lint yield of early-maturity upland cotton varieties is strikingly lower than that of middle- and late-maturity ones. How to effectively improve lint yield of early maturing cotton, becomes a focus of cotton research. Here, based on 72,792 high-quality single nucleotide polymorphisms of 160 early-maturing upland cotton accessions, we performed genome-wide association studies (GWASs) for lint percentage (LP), one of the most lint-yield component traits, applying one single-locus method and six multi-locus methods. A total of 4 and 45 significant quantitative trait nucleotides (QTNs) were respectively identified to be associated with LP. Interestingly, in two of four planting environments, two of these QTNs (A02_74713290 and A02_75551547) were simultaneously detected via both one single-locus and three or more multi-locus GWAS methods. Among the 42 genes within a genomic region (A02: 74.31–75.95 Mbp) containing the above two peak QTNs, Gh_A02G1269, Gh_A02G1280, and Gh_A02G1295 had the highest expression levels in ovules during seed development from 20 to 25 days post anthesis, whereas Gh_A02G1278 was preferentially expressed in the fibers rather than other organs. These results imply that the four potential candidate genes might be closely related to cotton LP by regulating the proportion of seed weight and fiber yield. The QTNs and potential candidate genes for LP, identified in this study, provide valuable resource for cultivating novel cotton varieties with earliness and high lint yield in the future.

Highlights

As one of the most important cash crops, upland cotton (Gossypium hirsutum L.) is widely cultivated around the world and supplies the most raw materials for the textile industry
Using six ML-genome-wide association study (GWAS) methods including mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, ISIS EM-BLASSO, and pKWmEB, we totally identified 45 quantitative trait nucleotides (QTNs) for lint percentage (LP) after removing duplicates
We found that the accessions from Yellow River Region (YRR) accounted for a larger proportion of two favorable allelic variations than those from Northwest Inland Region (NIR) and Northern Specific Early-Maturity Region (NSEMR), and the unfavorable allelic variations accounted for the largest ratio in the accessions from NSEMR (Figure 3A)

Summary

Introduction

As one of the most important cash crops, upland cotton (Gossypium hirsutum L.) is widely cultivated around the world and supplies the most raw materials for the textile industry. The increased average yield of cotton is mainly ascribed to the application of many improved varieties as well as precise farming technologies in China (Dai and Dong, 2014; Feng et al, 2017). It is well-known that upland cotton can be classified into early-, middle-, and late- maturity varieties based on the duration of their growth periods. Improving fiber yield is a major goal in Chinese early-maturity cotton breeding practice

Methods

Results

Conclusion