Association Analysis Of Salt Tolerance Traits With SSR And SNP Markers In Asiatic Cotton

This study was carried out to identify marker-trait association analysis using association analysis of 7 traits and one salt tolerance index,related to salt tolerance using SSR and SNP markers for 215 accessions of Asiatic cotton?Gossypium arboretum?.The traits related to salt tolerance like germination rate?GR?,fresh weight?FW?,stem length?SL?,water content?WC?,chlorophyll content?ChlC?,electric conduct?EC?and methylene dioxyamphetamine?MDA?,of 215 cotton accessions were screened out using 150mM salt concentration after 7 days of seed growth.In addition,according to the comprehensive index of salt tolerance,215 accessions were categorized mainly into four groups.Group 1 contained 12 accessions that were sensitive to high salt treatment?<0.6?,group 2 contained 26 accessions that were moderate tolerant to salt treatment?0.6?1.5?,group 3 includes 153 accession that were tolerant?1.5?2.5?,and group 4 had 24 accessions that were highly tolerant to salt treatment?>2.5?.The natural population was first classified into 3 main groups by phylogenic analysis,in which Group 2?G2?and Group 3?G3?represented the Yellow River and Yangtze River accessions respectively,while Group 1?G1?contained mixed cotton accessions which belongs to different cotton growing areas in china.The grouped accessions results were largely congruent with the breeding history and ecological region,which indicates the extensive genetic diversity of G.arboretum accessions both in phenotype and genotype.SSR marker-trait associations analysis revealed 90 marker-trait associations with significant level P<0.05.We used strict significant P value i.e.P<0.01 to find strong association and we obtained associations between 22 marker-trait.Among these 22 marker-trait associations,5 markers were associated with relative germination rate?RGR?,3 markers were associated with relative fresh weight?RFW?,4 markers were associated with relative stem length?RSL?,1 marker was associated with relative water content?RWC?,4 markers were associated with relative chlorophyll content?RChlC?,2 markers were associated with relative electric conduct?REC?,and 3 markers were associated with relative MDA?RMDA?.In this study,significant marker-trait associations were found which includes,NAU1023,NAU1099?both of these were associated RGR?,JES222?associated RChlC?,and NAU2783?associated REC?had high P value?P>3?.Two SSR markers?MUSS020 and NAU1375?were significantly associated with RFW,RMDA and RSL,while NAU3468 was significantly associated with RFW,RGR and RWC.The SNP markers associated with the seven traits and one salt tolerance index were identified based on the threshold value-LogP10?4.By applying the threshold of-log10 P?4.0,the 2062 SNP markers covered all 13 chromosomes and 100 SNP markers locations that were unknown.Among these 2062 marker-trait associations,61 markers were associated with RGR,187 markers were associated with RFW,255 markers were associated with RSL,370 markers were associated with RWC,190 markers were associated with RChlC,583 markers were associated with REC,335 markers were associated with RMDA and 81 markers were associated with comprehensive index of salt tolerance?CIST?.We focused on nine SNP rich regions sassociated RFW,RSL,RChlC,RWC and CIST for which MLMM analysis yield more significant associations taking into account-logio P values and the position of strong peaks in the Manhattan Plots.The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated RFW,RSL,RChlC,RWC and CIST.Some of the significant SNPs in the nine SNP rich regions were located in the candidate genes?Cotton_A37775,Cotton_A10865,Cotton_A10864,Cotton_A05853,Cotton_A21725 and Cotton_A21726?or near the candidate genes?Cotton_A35901,Cotton_A26218,Cotton_A15275,Cotton_A15276,Cotton_A28248,Cotton_A28249,Cotton_A22673 and Cotton_A22672?.The classification information derived from these studies may be used to facilitate the development of salt tolerant cotton accessions that could give economic yield in salinity prone areas.Remarkably,these markers,that are significantly correlated with improved salt tolerance and candidate genes can provides fundamental information,which will be useful for future molecular breeding of cotton,to release novel salt tolerant cultivars.