Analysis Of Genetic Diversity On Litchi(Litchi Chinensis Sonn.)Germplasm From Hainan And Identification Of Litchi Hybrids By SSR And InDel Markers

Litchi{Litchi Chinensis Sonn.) is one of the most important fruits in South China. Hainan is one of the original and major production region of litchi, has plenty of wild and cultivated litchi genotypes.Analysis of litchi genetic diversity will construct steady base for litchi genetic improvement and breeding. Cross breeding is a effective way to cultivate new varieties of litchi. The work to find an effective method for improving pollination efficiency and identifying hybrids, has vast importance to accelerate the crossbreeding process of litchi.In this study,a number of SSR and InDel markers were developed;we used these SSR and InDel markers to examine the genetic diversity of232wild,semi-wild, and cultivated litchi from Hainan.11Combination of hybrids were identified from2011to2014,and confirmed that the control pollination can significantly improve breeding efficiency,which became the basis for the next litchi breeding.The results are as follows:1. According to the EST sequences and genomic sequences obtained,a total of117EST-SSR primer pairs and34InDel primer pairs were designed.With6varieties of litchi DNA as templates, Selected30pairs of primers which can used to analyze the genetic diversity, including18pairs of SSR primers,12pairs of Indel primers; Selected8pairs of primers which can used to identify true hybrids before the hybrids with6litchi varieties as parents, i.e., Ziniangxi Wuheli Baitangying Feizixiao Sanyuehong and Xinqiumili.2. Application of18SSR and12pairs of InDel primers,we detected141loci in232litchi resources.Different primers to amplify loci between2to11,The average of polymorphic loci was4.7. The rate of139polymorphic loci was up to98.58%. Among the18pairs of SSR primers,11pairs had highly polymorphic primers,7pairs primers showed moderate polymorphism; But, for the12pairs of InDel primers,6pairs of them were of highly polymorphic primers.2pairs primers showed moderate polymorphism and4pairs primers showed low polymorphism. The average PIC,observed number of alleles, effective number of alleles, Nei’s gene diversity, Shannon’s genetic diversity were0.5166,1.9611,1.3539,0.2240and0.3574which showed that SSR and InDel primers could reveal the genetic differences between various litchi germplasms. Genetic differences exist between litchi germplasm, but the variation in level is not very high.3. UPGAM analysis was implied that, the similarity coefficients of litchi germplasm were among0.66～1.00.232cultivars could be divided into two groups in the similarity coefficients0.66. The majority of litchi germplasm from Hainan were gathered in a class when the test materials were divided into21groups in the similarity coefficients0.78.We saw that11wild litchi germplasm were clustering in7groups and62semi-wild litchi germplasm were clustering in17groups which indicated that the genetic diversity of wild and semi-wild litchi germplasm was very rich;74cultivated litchi germplasm and other cultivated litchi germplasm were clustered into one group by region, indicating small differences between litchi genetic variance which because of geographical isolation or artificial selection cultivation;The reason which some germplasm mixed was that litchi varieties were spreaded and breezed in origin, resulting in confusion of varieties. We had identified some germplasm which were the same cultivar but not use with different name.4. A total of11hybridization combinations were created by artificial or controlled pollination methods with six litchi varieties as parents, i.e., Ziniangxi Wuheli Baitangying Feizixiao Sanyuehong and Xinqiumili.including to use the control pollination with Ziniangxi as female and Wuheli as male,obtained2317F1generation.1666true hybrids from2317F1seedlings were identified using five pairs of SSR markers and three pairs of InDel markers.The true hybrid rates of the11hybridization combinations were different, with the average rate of true hybrids at71.90%. Some absent or new SSR and InDel loci in phenotypes of F1seedlings were appeared.Five homozygous makers were identified which could be used to identify the cross combinations of Ziniangxix Wuheli, WuhelixZiniangxi, Ziniangxi xFeizixiao, ZiniangxixSanyuehong, XinqiumilixWuheli, WuhelixXinqiumili, BaitangyingxWuheli and BaitangyingxSanyuehong. The results demonstrated that no significant difference between artificial pollination and controlled pollination.