Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

Weijie Tang; Jing Lin; Yanping Wang; Hongzhou An; Haiyuan Chen; Gen Pan; Suobing Zhang; Baowei Guo; Kun Yu; Huayong Li; Xianwen Fang; Yunhui Zhang

doi:10.1186/s12284-022-00594-0

Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

Rice (N Y). 2022 Sep 24;15(1):48. doi: 10.1186/s12284-022-00594-0.

Authors

Weijie Tang¹, Jing Lin¹, Yanping Wang¹, Hongzhou An², Haiyuan Chen¹, Gen Pan³, Suobing Zhang¹, Baowei Guo^{4

5}, Kun Yu¹, Huayong Li⁶, Xianwen Fang⁷, Yunhui Zhang^{8

9}

Affiliations

¹ Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China.
² The Key Laboratory of Crop Genetics and Breeding of Hebei Province, Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, People's Republic of China.
³ Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, People's Republic of China.
⁴ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China.
⁵ Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College of Yangzhou University, Yangzhou, People's Republic of China.
⁶ Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China. lhy@jaas.ac.cn.
⁷ Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China. xianwen_fang@hotmail.com.
⁸ Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, People's Republic of China. zyhrice@163.com.
⁹ Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, People's Republic of China. zyhrice@163.com.

Abstract

Background: Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown.

Results: Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others.

Conclusions: Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.

Keywords: KASP; Marker-assisted breeding; Rice; Variety identification.