Association Analysis of Salt Tolerance in Asiatic cotton (Gossypium arboretum) with SNP Markers

Abstract

Salinity is not only a major environmental factor which limits plant growth and productivity, but it has also become a worldwide problem. However, little is known about the genetic basis underlying salt tolerance in cotton. This study was carried out to identify marker-trait association signals of seven salt-tolerance-related traits and one salt tolerance index using association analysis for 215 accessions of Asiatic cotton. According to a comprehensive index of salt tolerance (CIST), 215 accessions were mainly categorized into four groups, and 11 accessions with high salinity tolerance were selected for breeding. Genome-wide association studies (GWAS) revealed nine SNP rich regions significantly associated with relative fresh weight (RFW), relative stem length (RSL), relative water content (RRWC) and CIST. The nine SNP rich regions analysis revealed 143 polymorphisms that distributed 40 candidate genes and significantly associated with salt tolerance. Notably, two SNP rich regions on chromosome 7 were found to be significantly associated with two salinity related traits, RFW and RSL, by the threshold of -log₁₀P ≥ 6.0, and two candidate genes (Cotton_A_37775 and Cotton_A_35901) related to two key SNPs (Ca7_33607751 and Ca7_77004962) were possibly associated with salt tolerance in G. arboreum. These can provide fundamental information which will be useful for future molecular breeding of cotton, in order to release novel salt tolerant cultivars.

Keywords: Gossypium arboretum; association mapping.; salt tolerance; single nucleotide polymorphisms.

Figure 1

Relative value frequency distribution diagram of seven salt tolerance traits and one salt tolerance index of 215 G. arboreum accessions.

Figure 2

Quantile-quantile plots of versus expected −log₁₀P values of GWAS result. The red dashed line in each plot represents an idealized case where theoretical test statistics quantile match simulated test statistic quantile. (a) Relative germination rate (RGR). (b) Relative fresh weight (RFW). (c) Relative stem length (RSL). (d) Relative water content (RWC). (e) Relative chlorophyll content (RChlC). (f) Relative electric conductivity (REC). (g) Relative MDA (RMDA). (h) Comprehensive index of salt tolerance (CIST).

Figure 3

GWAS results for RFW and RSL, and analysis of the peaks on chromosome 7 (Group 1 and Group 2). (a) Manhattan plot for RFW. The horizontal line represents the significant threshold (−log₁₀P = 4). The pink color surrounds represent SNP rich regions (Group 1 and Group 2). (b) Manhattan plot for RSL. The horizontal line represents the significant threshold (−log₁₀P = 4). The pink color surrounds represent SNP rich regions (Group 1 and Group 2). (c) LD surrounding the peak of Group 1. (d) LD surrounding the peak of Group 2. (e) Phenotypic differences for RFW based on the key SNP (Ca7_33607751) of Group 1. (f) Phenotypic differences for RSL based on the key SNP (Ca7_33607751) of Group 1. (g) Phenotypic differences for RFW based on the key SNP (Ca7_77004962) of Group 2. (h) Phenotypic differences for RSL based on the key SNP (Ca7_77004962) of Group 2.

Figure 4

GWAS results for RChlC and analysis of the peaks on chromosome 4, 9 and 11. (a) Manhattan plot for RChlC. The horizontal line represents the significant threshold (−log₁₀P = 4). The pink color surrounds represent SNP rich regions (Group 3, Group 4, Group 5 and Goup 6). (b) LD surrounding the peak of Group 3. (c) LD surrounding the peak of Group 4. (d) LD surrounding the peak of Group 5. (e) LD surrounding the peak of Group 6. (f) Haplotypes in Group 3. (g) Haplotypes in Group 4 (h) Haplotypes in Group 5. (i) Phenotypic differences of RChlC between two haplotypes in Group 3. (j) Phenotypic differences of RChlC between two haplotypesin Group 4. (k) Phenotypic differences of RChlC between two haplotypesin Group 5. (l) Phenotypic differences for RChlC based on the key SNP (Ca11_47011718) of Group 6.

Figure 5

GWAS results for RWC and analysis of the peak on chromosome 7. (a) Manhattan plot for RWC. The horizontal line represents the significant threshold (−log₁₀P = 4). The pink color surround represents SNP rich region (Group 7). (b) LD surrounding the peak of Group 7. (c) Haplotypes in Group 7. (d) Phenotypic differences of RWC between two haplotypes.

Figure 6

GWAS results for CIST and analysis of the peaks on chromosome 2 and 11. (a) Manhattan plot for CIST. The horizontal line represents the significant threshold (−log₁₀P = 4). The pink color surrounds represent SNP rich regions (Group 8 and Group 9). (b) LD surrounding the peak of Group 8. (c) LD surrounding the peak of Group 9. (d) Haplotypes in Group 8. (e) Haplotypes in Group 9. (f) Phenotypic differences of CIST between two haplotypes in Group 8. (g) Phenotypic differences of CIST among three haplotypes in Group 9.