Identification Of Flowering-related Genes And Analysis Of Domestication Selection In Cotton

Cotton is one of the important cash crops in our country,its main product cotton fiber is an important raw material of textile industry.China is the major cotton producer and consumer,but not the country of origin of cotton.The wild tetraploid cotton originated from the low latitude area in America is a photoperiod sensitive short-day plant,but the widely cultivated cotton is a photoperiod insensitive neutral plant.Flowering is the key turning point from vegetative growth to reproductive growth.Early flowering can shorten the growth period,is conducive to the rational arrangement of planting crops,and reduce the contradiction with grain for land.Therefore,identifying flowering-related genes in cotton and exploring the genetic rules and regulatory networks for their domestication and improvement have important theoretical guiding significance for de novo domestication of cotton and cultivation of early maturity cotton varieties.In this study,the genes of flowering regulatory pathways in Arabidopsis thaliana were used as seed sequences to identify homologous genes of corresponding flowering pathways in cotton varieties such as G.raimondii,G.herbaceum,G.arboreum,G.hirsutum and G.barbadense.Besides,three gene families(PHY,COL and PEBP)are analyzed in terms of phylogeny,gene structure,regulatory elements and expression pattern;The patterns and laws of domestication and selection of flowering related genes in cotton were studied based on a large number of genome re-sequencing data;The response patterns of flowering-related genes to light treatment in wild and cultivar varieties were analyzed using long-day and short-day transcriptome data from wild and modern cultivar of upland cotton.The main results of this paper are as follows:1.A total of 260,286,297,570,and 574 flowering-related genes were identified in five cotton species including G.herbaceum,G.arboreum,G.raimondii,G.hirsutum and G.barbadense.Among them,17 genes including ATC,SMZ,SNZ,TEM2,TSF,GID1 C,CCA1,PHYD,CPK6,MAF1,MAF5,TOE2,FLC,VEL2,VEL3,VIN3 and GA20ox3 were not identified in the five cotton species.2.Bioinformatics analysis of PHY,COL,PEBP gene families.Phylogenetic tree analysis showed that PHY family,COL family and PEBP family could be divided into four,three and five subfamilies,respectively.Gene structure analysis showed that PHYs gene contained four to six exons;COLs genes all contain two exons;PEBPs genes contain two to four exons.The analysis of expression patterns showed that Gh PHYs,Gh COLs and Gh PEBPs exhibited certain tissue-specific expressions in upland cotton.3.The results of genetic diversity analysis showed that the pi of flowering-related genes via photoperiod,vernalization and gibberellin in cultivar were significantly lower than those of wild,but the floral pathway integrators and the flowering-related genes via autonomous were significantly increased in upland cotton.The pi values of floweringrelated genes via photoperiod,gibberellin,floral pathway integrators in landrace were higher than that in cultivar.The pi of flowering-related genes related to age,vernalization,and autonomous regulation were higher in the cultivar than in the landrace in pima cotton.Among the flowering-related genes of upland cotton,the genetic differentiation coefficient of 406 genes between the wild and the landrace was greater than 0.25,and that of 394 genes between the landrace and the cultivar was greater than 0.25,which indicated that these genes had great genetic differentiation among populations.The coefficient of genetic differentiation of 110 genes of flowering-related genes in pima cotton between landrace and cultivar was greater than 0.25,indicating that these genes had great genetic differentiation between landrace and cultivar.4.Transcriptome data analysis of wild and domesticated upland cotton under different sunlight length treatments found that,the comparison between wild and acclimated materials in the early,middle and late periods of long and short sunshine revealed that there were 410,623,542,274,470 and 586 differentially expressed genes in common;Cascot L7,Maxxa,TX2094,TX2095 had 1994,1361,1670,806 unique differentially expressed genes respectively between the three time periods of long and short sunshine,morning,afternoon and evening;among them,there were 107 differentially expressed genes related to flowering,which were mainly concentrated in the photoperiod regulation pathways.GO analysis and KEGG analysis showed that DEGs was mainly enriched in some pathways related to circadian rhythm and photoperiod regulation,indicating that photoperiod regulation played an important role in cotton flowering.