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| 一个控制陆地棉株高主效QTL的遗传研究
摘 要
棉花是世界上不可或缺的纤维经济作物，在诸多领域发挥着重要作用。株高作为一个关键的农艺性状，能够直接影响甚至决定棉花的经济产量，并且合适的株高能够在机械化采收、降低化学污染、提升肥料利用水平以及抗倒伏能力等多个方面发挥重要意义。因此通过遗传学手段改良棉花株高十分迫切，现阶段棉花株高研究中多基于突变体以及利用分离群体进行QTL定位，随着高通量测序技术的成熟和普及，全基因组关联分析（关键词：陆地棉，株高，全基因组关联分析，精细定位，功能验证
Abstract
Cotton is an indispensable fiber economic crop in theworld, which plays an important role in many fields. As a key agronomic character,plant height can directly affect or even determine the economic yield of cotton. The appropriate plant height can play a key role in mechanized harvesting,reducing chemical pollution, improving the level of fertilizer utilization and lodging resistance. Therefore, it is urgent to cultivate cotton varieties with suitable plant height by genetic means.At present, cotton plant height research is mostly based on mutants and using segregated populations for QTL mapping. With the maturity and popularization of high-throughput sequencing technology, the combination of GWAS and segregated populations is an efficient methodto study quantitative traits related genes and genetic characteristics.
In this study, the natural population of 1245 upland cotton varieties was used as material to carry out genome sequencing and multi-environmental phenotypic investigation. On this basis, the genome wide association study （GWAS） was carriedout, and the candidate interval of ~ 300kb with significant correlation with plant height was identified in the region of A01 chromosome 3.60-3.90Mb.The genotypic heat map was drawn based on the SNP loci in the interval and the materials were divided into five haplotypes （Hap1-Hap5）. Based on the plant height analysis of different haplotypes,Hap1 was defined as Hap-Short （Hap-S）, Hap2 was defined as Hap-Medium （Hap-M）, and Hap4 and Hap5 were defined as Hap-Tall （Hap-T）. Combined with the previous phenotypic data,six extreme plant height materials （three haplotype Hap-S and three haplotype Hap-T） were selected from 1245 materials and planted in the field in 2019. The plant height of the above materials was continuously monitored.It was found that the bud stage was the key period for plant height differentiation of different types of materials. The investigation on the length and number of stem nodes showed that the difference in plant height between Hap-S and Hap-T was the result of the joint action of stem node length and stem node number. At the same time, the inverted third internodes of the two types of materialswere sampled at the bud stage in 2019,and it was found that the cell length of Hap-T type materials was significantly longer than that of Hap-S type materials. It is considered that the difference in cell length is the cytological basis for the plant height of Hap-S and Hap-T materials.
After determining the candidate interval, 18 genes in the interval were analyzed.Stem tips of two types of materials were sampled at the bud stage with significant plant height differentiation, transcriptome sequencing and qRT-PCR analysis were carried out,and three candidate genes were obtained: Gh_A01G037400, Gh_A01G038100 and Gh_A01G038200. The extreme plant height materials' Tornado' and '6086' of Hap-S and Hap-T were planted in greenhouse to further verify the selected candidate genes,and it was found that only Gh_A01G038100 and Gh_A01G038200 had the same trend of gene expression difference as the previous analysis. In order to further narrow the candidate interval to determine candidate genes,the F2 segregation population prepared by 'Tornado' and '6086' was used for fine mapping, and a total of 3 QTL loci were detected, explaining the highest phenotypic variation of 22.36% and the lowest of 4.50%.Gh_A01G038100 and Gh_A01G038200 are located in the QTL （qPH-A01-2） which explains the highest phenotypic variation. Combined with the previous analysis,we further identified the candidate genes as Gh_A01G038100 and Gh_A01G038200.
In order to further study the role of the above two genes in the formation of uplandcotton plant height, the plant height of plants inoculated with silent Gh_A01G038100virus increased by gene silencing induced by VIGS （Virus Induced Gene Silencing）,while the plant height of plants inoculated with silent Gh_A01G038200 virus did not change. After heterologous overexpression of Gh_A01G038200 in Arabidopsis thaliana,we found that the plant height and branch number of overexpressed plants decreased significantly. It is preliminarily concluded that Gh_A01G038100 may be the key gene to control upland cotton plant height.
In this study, from the perspective of upland cotton population,this study used the largest scale （1245 materials）of whole-genome resequencing (10X) genotype data combined with multi-environmental phenotype data to locate high major QTLs for upland cotton plants. Subsequent cross-validation of the segregated populations and functional verification showed that Gh_A01G038100 is the major gene controlling the height of upland cotton. This study provides theoretical support for the improvement of upland cotton plant type and the realization of high-efficiency mechanical harvesting.
Keywords: Upland cotton, plant height, GWAS, fine mapping, functional verification
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ther study the role of the above two genes in the formation of upland cotton plantheight, the plant height of plants inoculated with silent Gh_A01G038100 virus increased by gene silencing induced by VIGS （Virus Induced Gene Silencing）,while the plant height of plants inoculated with silent Gh_A01G038200 virus did not change. After heterologous overexpression of Gh_A01G038200 in Arabidopsis thaliana,we found that the plant height and branch number of overexpressed plants decreased significantly. It is preliminarily concluded that Gh_A01G038100 may be the key gene to control upland cotton plant height.
In this study, from the perspective of upland cotton population,this study used the largest scale （1245 materials）of whole-genome resequencing (10X) genotype data combined with multi-environmental phenotype data to locate high major QTLs for upland cotton plants. Subsequent cross-validation of the segregated populations and functional verification showed that Gh_A01G038100 is the major gene controlling the height of upland cotton. This study provides theoretical support for the improvement of upland cotton plant type and the realization of high-efficiency mechanical harvesting.
Keywords: Upland cotton, plant height, GWAS, fine mapping, functional verification
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