Association Analysis Of Phenotypic With SSR Markers In Cassava

SSR (Simple Sequence Repeats) primers were used to research genetic diversity and association mapping among149germplasm cassava, by scaning the genome polymorphic loci, in this study. Besides,6quantitative traits which including plant height, tuber weight, tuber number, total weight, dry matter ratio, PPD (Postharvest Physiological Deterioration) and11morphological markers that including leaf color, petiole color, leaf shape, tuberization concentration, constriction, epidermal (rough or smooth, tuber skin color, tuber epidermis color, stem endothelial color, stem skin color, young stem color were also investigated. Meanwhile, the genetic diversity, the principal component and the population structure were analysed. Finally, by using the association mapping method, lots of SSR polymorphic loci which was associated with the important physiological and indicators of cassava was obtained, and provide a reference for cassava molecular marker-assisted breeding in future. The main results are as followings:1. Analyze diffirent locus in349SSR Polymorphic locis of germplasm cassava by using Summary statistic function of POWERMARKERv3.0and Frequence function of GENALEX2.10e software. The maximum of Locus genetic diversity is0.55, the minimum is0.0000and the mean is0.35. The maximum of polymorphic information content (PIC) is0.47. The minimum is0.00and the mean is0.28. The mean of differences alleles of per locus (Na) is2.00, the mean of effective number of alleles (Ne) is1.60, the mean Shannon index (I) is0.53, the mean Nei’s genetic diversity (h) is0.35, and the mean Unbiased Nei’s genetic diversity (uh) is0.35.2. Clustering analysis is performed on the149germplasm cassava by SSR molecular marker. The result is that the range of variation between samples of genetic similarity coefficient(GS) is between0.36-0.84, the mean is0.65. When the genetic similarity coefficient (GS) is0.64, the germplasm resources can be divided into five groups, including the SC205(CK) separately as a pop, and the remaining four are named popl, pop2, pop3, pop4, and the number of each groups’members are4,5,58,81.3. The148cases of cassava germplasm, besides CK, are done principal Composition analysis with the GENALEX6.2software PCA subroutine and the NTSYSPC2.10e software Eigen subroutine, found that the two group-divided ways are the same, and the results are the same with NTSYSPC2.10e UPGMA Tree clustering analysis, that is, four groups. So, SSR markers indicate the reliability.4. The148germplasm cassava are divided into four groups. The percentage of polymorphic loci ordering pop4> pop3> pop2> popl. The different in allele (Na), the effective number of alleles (Ne), the Shannon index (I), the Nei’s gene diversity (h), the unbiased Nei’s gene diversity (uh) and the percentage of polymorphic loci (%P) in Pop3and pop4are higher than the mean. So the gene diversity of pop3and pop4is higher than popl and pop2. Significant condition of p<0.01, the gene differentiation degree (PhiPT) was0.19, gene flow (Nm) was2.18, It shows that the four groups have strong gene flow.5. The principal component analysis shows that, the The comprehensive performance of61.74%of germplasm cassava are excellent than SC205(CK), and the order of the comprehensive effect on yield of5traits that related to the yield is: the total weight>the tuber weight> the plant height> the number of tubers> the dry matter ratio.6.Analyze54,947combinations of the proceeds from the test sites332Polymorphic locis, in remarkable condition of r2>0.05, P<0.05, digit combination to achieve significant LD point for3,714. Significant condition of P <0.0001, r2≥0.7,15strong linkage disequilibrium locus combinations are detected.7.By using association analysis, ten significantly associated quantitative traits loci(plant height, tuber weight, tuber number, total weight, dry matter ratio, PPD(3d)> PPD(7d)、PPD(12d)、PPD (17d)、PPD(24d) and eleven significantly associated morphological markers loci(leaf shape, Petiole color and so on) are found. Associated analysis is with application PCA+K+MLM model at P=5%allele frequency filter conditions. There are332Polymorphic locis involved in association analysis with21traits. A total of151Polymorphic locis are associated with21traits. The average of variations markedly explaining rate is3.71%, range from1.69%-9.96%. At P<0.001condition, three SSR locis associated significantly to the skin (rough or smooth), respectively, are m337-c、m304-d and m324-d. The plant height significantly associated loci is m224-c and the petiole color significantly associated loci is m299-a.