Comparative Study on the Indica-japonica Differentiation of Oryza L. Resources in Yuanjiang, Yunnan Province by Cheng’s Index and InDel Molecular Index

PurposeTo study the indica-japonica characteristics and the degree of indica-japonica differentiation of Oryza rufipogon in Yuanjiang, Yunnan Province and its consanguineous introgression line, providing a theoretical basis for exploring the origin, evolution, genetic differentiation, breeding and utilization of O. rufipogon.

MethodsUsing the Cheng ’s index and InDel molecular index to analyze the characteristics of indica-japonica from O. rufipogon in Yuanjiang, Hexi 35 and 354 introgression lines from the phenotype to molecular level.

ResultsThe analysis result of Cheng ’s index showed that the total score of O. rufipogon was 11, which was indicaclinous, and the total score of Hexi 35 was 24, which was japonica. Among 354 introgression lines, there were 179 indica, 76 indicaclinous, 25 japonica and 74 japonicaclinous. By InDel molecular index method, it was found that the indica gene frequencies of O. rufipogon and Hexi 35 were 0.32 and 0.04, respectively, belonging to japonicaclinous and typical japonica. Among 354 introgression lines, there were 113 typical indica, 84 indica, 36 indicaclinous, 29 intermediate types, 21 japonicaclinous, 24 japonica and 47 typical japonica. The results of Cheng’s index and Indel molecular index showed that the fitting degree of the two methods was as high as 92.42%, and there was only a deviation in the classification results of indica-japonica types of O. rufipogon and 26 introgression lines.

ConclusionThe results of Cheng’s index and InDel molecular index were basically consistent. The combination of the two methods can effectively analyze the indica-japonica characteristics of O. rufipogon and its introgression line offspring. There are some differences in the indica-japonica characteristics of O. rufipogon at the phenotypic and molecular levels, which may be related to the incomplete indica-japonica differentiation of O. rufipogon. The progenies of introgression lines of O. rufipogon in Yuanjiang have rich indica-japonica types and obvious differentiation. They are not only important breeding materials, but also valuable resources in the origin, evolution and classification of O. rufipogon.