| Cotton (Gossypium spp.) is a major cash crop for both textiles and food. Upland cotton(Gossypium hirsutum L.) accounts for >95% of world cotton production. However, as a salt-tolerance pioneer crop,cotton-growing areas are subject to long time and high concentration salt stress, which can impede cotton growth and production. Therefore, the study of excavate salt-tolerance germplasms, exploit allelic variations and molecular design breeding in cotton breeding will play an important role in increasing salt-tolerance study.This study used 304 representative upland cotton cultivars as research materials.Through salt stress experiments, this study screened salt-tolerance germplasms, analysed the relationships among 10 salt-tolerance traits,estimated the genetic diversity,population structure and linkage disequilibrium in 304 upland cotton cultivars with 145 SSR loci distributed over all 26 chromosomes, analyzed the association loci with 10 salt-tolerance traits, screened favorable alleles and simulated molecular design breeding. The main results are included as follows:Identification of salt resistance of 304 upland cotton cultivars1. Screening and sorting of 304 Upland cotton cultivars.According to eco-geographical growing region, 304 representative upland cotton cultivars could be divided into 5 groups as Yellow River (177), Yangtze River (78),North-west China Inland (23), North China Early Maturity group (16) and 10 upland cotton cultivars introduced from America, as a control group, call basal germplasm group.By NaCl stress concentration gradient test, 150 mM NaCl was further confirmed to be suitable for salt tolerance evaluation of upland cotton cultivars. Factor and cluster analysis results showed that 43 cultivars were advanced salt-tolerance eg Yumianl5, Zhongzhimian2,Sumian20 and so on, 114 cultivars were medium salt-tolerance eg zhongzhimian8,ekangmian2, zhongzhimian86-4 and so on, 116 cultivars were junior salt-tolerance eg yumian112, wanmianl7, 86-1 and so on, 31 cultivars were salt-sensitive eg kekangmian2,shumianl,lumianyan32 and so on.2. The distribution of salt resistance among different geographic eco-types regionsUpland cotton cultivars from Yellow River, Yangtze River, North-west China Inland and North China Early Maturity region had the following characteristics: the average salt resistance of different geographic eco-types regions were decreased; The percentage of advanced salt-resistance cultivars of each geographic eco-type were decreased and the percentage of salt-sensitive cultivars of each geographic eco-type were increased.Association analysis for salt-resistance traits in upland cotton3. Genetic diversity analysis.514 alleles were detected in total by 145 SSRs in the population studied, with an average of 3.5 alleles per marker locus, ranged from 2-11. The number of alleles of 117 SSRs were from 2 to 4, it means the genetic diversity of the 304 upland cotton cultivars in this study was at a lower level. The average gene diversity of population were 0.365,ranged from 0.007-0.781. An average of PIC was 0.319, ranged from 0.007-0.747.4. Analysis of population structure and linkage disequilibrium.Seven subpopulations were found in the population constituted of 304 upland cotton cultivars, by using two methods, i.e., STRUCTURE 2.3 analysis method and the Neighbor-Joining cluster methos. Linkage disequilibrium at certain extent was found between SSR marker loci either intra-chromosome or inter-chromosome. Relative higher levels of LD (D’> 0.5) mainly distributed in chromosome A7, D7, D8, D10, All and A12.The average genetic distance of LD blocks extended was 54.99 cM. A biological explanation for sub-population clusters in 304 upland cotton cultivars was completed with chi-square test, and the results showed that 304 upland cotton cultivars were composed of seven sub-populations, which associated with their five geographic eco-types, indicating the classification of geographic eco-types was of sound genetic bases.5. Association analysisAt the p<0.05 level, a total of 95 significant associations were detected between 60 SSRs and ten salt-resistance related traits. Almost all cotton chromosomes were detected except D4. The number of SSRs associated with RCC, RPH, RRDM, RSDM, RSOD,RPOD,RCAT,RMDA,RGR and RGP were 9, 12, 12, 8, 8, 11,1,17, 8 and 9, and the distribution of chromosome number were 8, 9, 10, 7, 7, 7, 1, 13, 7 and 7, respectively.6. Specific alleles in advanced salt-resistance and salt-sensitive cultivarsBased on the results of factor and cluster analysis and phenotypic effects, we found 6 positive alleles and 4 negative alleles existed only in advanced salt-resistance cultivars, and 9 negative alleles and 2 positive alleles existed only in salt-sensitive cultivars. For example,positive alleles NAU483-B, NAU1042-B and negative allele NAU1369-G existed only in advanced salt-resistance cultivars, and negative alleles BNL1231-C and NAU1042-G existed only in salt-sensitive cultivars.Mining favorable alleles and breeding utilization7. Mining favorable allelesFrom 60 associated SSRs, 117 alleles were identified as elite alleles, and 16, 16,18,12,11,18,1,35, 16 and 19 favorable alleles for RCC,RPH,RRDM,RSDM,RSOD,RPOD,RCAT, RMDA, RGR and RGP were identified, respectively. This part of research take into account the value of phenotypic effect and the number of associated traits to evaluate favorable alleles, take 17 favorable alleles as examples to analysis and research their characteristics.8. Simulation of molecular design breedingFirst choosed acceptor cultivars of molecular design breeding. Elite cultivars were usually developed by gradually pyramiding favorable alleles in breeding history. This part of research calculated the total of favorable alleles for each upland cotton cultivar, and confirmed 13 cultivars as acceptor eg Dongting1, Ejing92, Emianl4, Lu458, Sumian20,Sumian8 and so on. Then simulated molecular design breeding, and the results were as follows: under single cross condition,optimal donor was yan1113, optimal single cross pattern was (dongtingl/zhongmiansuo44xyan1113) and 53 elite alleles were combined;under three-way cross condition, optimal donors were sumian8 and yan1113, optimal three-way cross pattern was (dongting1×sumian8) ×yan1113 and 56 elite alleles were combined; under four-way cross condition, optimal donors were zhongmiansuo40,wanmian3 and yan1113, optimal four-way cross pattern was [(Xin80477 ×zhongmiansuo40) × wanmian3] × yan1113 and 59 elite alleles were combined. |
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