QTL Mapping And Candidate Genes Identification Of Early Maturity Traits In Gossypium Hirsutum L.

Cotton（Gossypium spp.）is the main source of natural fiber and an important oil crop in the world.In recent years,it has also been used as a particular flower material.It plays a vital role in the national economy and people’s lives.However,with the decreased of cultivated land area in China,the conflict between cotton and grain competition is increasingly prominent,and the area of cotton planting in inland has gradually decreased,which has caused severe challenges to cotton production of China.The early maturity of cotton can shorten the growth period,and then achieve double cropping,increase the land multiple cropping index,and effectively alleviate the contradiction between grain and cotton.Therefore,early maturity have always been an important target trait for cotton breeding.The early maturity of cotton is a complex quantitative trait,which is greatly affected by environmental factors,such as temperature and photoperiod.It is important to research the inheritance of early maturing traits for breeding.Based on our preliminary work,we constructed the BC₃F₂backcross population using the early maturing variety LMY19,and constructed a high-density genetic map for mapping the cotton early maturity related QTLs using In Del markers developed based on DNA resequencing result of the mapping parents.Combining transcriptome data under different photoperiod conditions,we further identify candidate genes associated with the cotton early maturing traits related QTLs.The main conclusions are as follows:1.The early-maturing variety LMY19 and the late-maturing variety LMY37 were used as parents to construct the BC₃F₂ population through hybridization and backcross.At different developmental stages,the flowering period,the rate of open bolls,the node of first fruiting branch,the plant height and the number of bolls per plant were investigated in LMY19,LMY37 and the backcross group BC₃F₂（856 individuals）.The phenotypic data showed that maturity traits were significantly different between parents,and the five early maturing traits were normally distributed in the backcross population BC₃F₂,indicating that cotton early maturing traits are typical quantitative traits.2.Based on our primarily mapped early-maturity-associated genomic region（the physical distance is:20.29Mb-39.02Mb）located on the D03 chromosome of Gossypium hirsutum L.,we use the resequencing data of the mapping parents to develop In Del markers in the target chromosomal segment for genetic map construction by genotyping 856 individuals in the BC₃F₂ population.The genetic map of the target region of the encrypted D03 chromosome was constructed using the software Joinmap4.0.Combining the phenotypic data of five early maturity traits,the QTL mapping of cotton early maturity related traits was performed using Win QTLCart 2.5software.A total of 9 QTLs related early maturity traits were identified on chromosome D03,and the phenotypic variation rate explained was between 7.57%and 29.67%,one of them is the flowering time（q FT-D03-1）,three are the rate of open bolls（q ROB-D03-1,q ROB-D03-2,q ROB-D03-3）,and three are the node of first fruiting branch（q NFFB-D03-1,q NFFB-D03-2,q NFFB-D03-2）,two are plant height（q PH-D03-1 and q PH-D03-2）,and the candidate interval is reduced to 25.86Mb-28.33Mb。3.Combining with gene functional annotation and q RT-PCR results,four candidate genes that might be related to early maturity traits of cotton were preliminarily determined in the candidate interval by using QTL positioning results.Among them,Gh＿D03G1269 gene was located near Indel106 marker,which closely linked with plant height related QTL（q PH-D03-1）.Four candidate genes were further functionally verified by virus-induced gene silencing（VIGS）.After the silencing of Gh＿D03G1269gene in the parent LMY37,the plant height was significantly higher than that of the negative control,speculating that the gene negatively regulated the plant height（biomass related traits）in upland cotton.4.In order to verify the relationship between Gh＿D03G1269 and early maturity in cotton,we use natural population comprised 134 individual lines for genotyping analysis of single nucleotide mutation by 80K Gene Chip.The results showed 78materials have the same genotype with LMY37 and 50 materials have the same genotype with LMY19 while 6 are heterozygous types.Association analysis of the phenotyping data of the natural population,including budding stage（Bud period,BP）and flowering period（Flower Time,FT）showed that the two genotypes of budding period and flowering period were significantly different,it is speculated that this gene may play a role in cotton maturity.5.Flowering stage is the most direct character to judge the early maturity of cotton,and photoperiod regulation is one of the important ways to regulate the flowering of plants.To explore photoperiod influence on cotton flowering,we set up the different photoperiod（long day:16 h/8 h,28℃/25℃,short day:10 h/14h,28℃/25℃）conditions on the early and late maturity varieties and investigate the date of the first bud.The results showed that the early-maturing variety LMY 19 was more sensitive to photoperiod and the budding of LMY19 in long-day condition is about 19 days earlier than that in short-day condition.On this basis,the seedlings with the same growth were collected at the one-leaf stage,two-leaf stage,three-leaf stage and five-leaf stage respectively for transcriptome sequencing.The results showed that among the 63124genes annotated in the genome,30500 genes were co-expressed in all conditions,and2140 genes were period-specific.Using the weighted gene co-expression network analysis（WGCNA）method,a total of 16 different gene co-expression modules were constructed,one of which was corresponding to the traits of early and late maturing varieties.Meanwhile,we also explored and analyzed the candidate key genes of this module.