Effects of on-farm conservation and germplasm bank conservation on allelic variation in Yunnan local rice varieties based on SSR molecular marker analysis

【Objective】This study analyzed the allelic variation of corresponding local rice varieties under on-farm conservation and germplasm bank conservation by SSR markers,aiming to assess their impacts on the genetic diversity of rice germplasm resources. The findings would provide theoretical basis for the effective conservation of local varieties genetic diversity and the selection of preservation strategies. 【Method】Twelve germplasm bank conservation local varieties（Variety Name-1） and their corresponding on-farm conservation local varieties（Variety Name-2） were used as materials. A total of 24 local rice samples（12 pairs） were analyzed for genetic diversity and allelic variation using 72 SSR markers. 【Result】A total of 490 alleles were detected in the 24 samples,with a range of 4 to 12,and an average of 6.8. And the Nei’s gene diversity index ranged from 0.337 to 0.910,with an average of 0.769. The number of alleles,specific allele and effective alleles under on-farm conservation were slightly lower than germplasm bank conservation. However,Nei’s gene diversity index was marginally higher,indicating that the genetic diversity was slight decline under on-farm conservation. Xiaobainuo-2 and Landigu-2 exhibited no allelic variation sites at the markers RM333 and RM213 respectively under onfarm conservation. Xiaobainuo-2,Laojiangnuo-2 and Laoshuyua-2 displayed homozygous allelic variations at the markers RM349,RM18 and RM333 respectively, which revealed that the allelic variation sites would be lost under on-farm conservation. The genetic similarity coefficients among the 12 groups of local rice materials ranged from 0.222 to 0.917,with the highest in Xianggu and the lowest in Xiaobainuo. At a genetic similarity coefficient value of 0.205,the tested local rice materials could be clustered into indica and japonica categories,and each corresponding local rice materials further clustered into smaller categories,indicating a high degree of genetic similarity and correspondence among the tested varieties. A total of 260 allelic variation sites were detected among the 24 local rice materials,with a range of 6 to 57. Among these,28 were associated with stress resistance,25 with fertility,33 with disease and pest resistance,and 26 with yield and nutrition-related traits. And the theoretical yield has increased under on-farm conservation, it indicated that genetic variations produced under on-farm conservation might develop in the direction of enhancing adaptability to increase yield. 【Conclusion】Under on-farm conservation,the alleles homozygosity and loss of partial local rice varieties are intrinsic factors reducing genetic diversity. A large number of genetic variations are generated on functional linkage markers such as fertility,disease and insect resistance,stress tolerance,yield and nutrition efficiency, with change trends of reduced plant height and increased yield. The ability of local rice varieties to adapt to natural ecological and socio-environmental pressures are enhanced. It is indicated that on-farm conservation is one of the effective ways to protect the diversity of local rice resources.