Core EST-SSR Marker Selection Based on Genetic Linkage Map Construction and Their Application in Genetic Diversity Analysis of Litchi (Litchi chinensis Sonn.) Germplasm Resources

This paper reports on the development of EST-SSR markers on a large-scale and further selection of their core markers based on the genetic mapping and application in following analyses of genetic diversity and germplasm identification in litchi. The results showed polymorphisms from 242 out of 784 pairs of EST-SSR primers applied to populations of 'Maguili' and 'Sanyuehong', with 84 individuals of hybrid progeny. The genetic linkage map was constructed and 8 linkage groups were obtained, on which 78 EST-SSRs are located and 34 markers whose genetic distances were greater than 3 cM were designed as the core markers. The core markers were applied to detect the genetic diversity of the resources and were used to identify hybrid progenies from two newly made crossing populations. The cluster analysis of 416 litchi samples collected from different regions of China indicated that the similarity coefficients ranged from 0.44 to 1.0, which suggested a high genetic diversity exists for litchi germplasm. The 416 samples could be classified into 2 and 37 groups at the similarity coefficient of 0.44 and 0.684, respectively. Incidentally, there were more than 30 samples which were identified as homonyms and/or synonyms. The cluster analysis was also applied to accessions from different provinces by POPGENE32 software and the evolution event for litchi resources is discussed. Six core markers were successfully applied to identify true hybrids from two population seedlings of 'Xuehuaizi' x 'Guiwei' and 'Xuehuaizi' x 'Jiaohesanyuehong', respectively.