Abstract
Rice has been cultivating and utilizing by humans for thousands of years under diverse environmental conditions. Therefore, tremendous genetic differentiation and diversity has occurred at various agro-ecosystems. The significant indica–japonica differentiation in rice provides great opportunities for its genetic improvement. In the present investigation, a total of 42 polymorphic InDel markers were used for differentiating 188 rice landraces and two local varieties of Chhattisgarh, India into indica and japonica related genotypes based on ‘InDel molecular index’. Frequency of japonica alleles varied from 0.11 to 0.89 among landraces. Results revealed that 104 rice landraces have indica type genetic architecture along with three tested indica cultivars Swarna, Mahamaya and Rajeshwari. Another 60 landraces were placed under ‘close to indica’ type. It was found that three rice landraces i.e. Kalajeera, Kapri, Tulsimala were ‘close to japonica’ type and 21 landraces were ‘intermediate’ type. The result from the calculation of ‘InDel molecular index’ was further verified with STRUCTURE, AMOVA, PCA and cluster analysis. Population structure analysis revealed two genetically distinct populations within the 190 rice landraces/genotypes. Based on AMOVA, ‘intermediate’ type, ‘close to japonica’ type and Dongjinbyeo (a japonica cultivar from Republic of Korea) displayed significant genetic differentiation (ɸPT = 0.642, P = 0.000) from ‘indica’ and ‘close to indica’ groups. The PCA scatter plot and dendrogram demonstrated a clear pattern of two major group differentiations. ‘Close to japonica’ type and ‘intermediate’ type landraces/genotypes were grouped with Dongjinbyeo and formed a separate cluster at 30% Jaccard’s similarity level from rest of the landraces/genotypes which were ‘close to indica’ or ‘indica’ type. Such a significant genetic differentiation among the locally adapted landraces could be exploited for the development of rice varieties introgressing higher yield potential and better plant types of japonica type as per the need of consumers and rice traders.
Highlights
Rice (Oryza sativa L.) is one of the most important food crops in the world and supports the requirement of staple food for almost half of the world’s population
The marker R1M37 showed dominant reaction, while rest of the insertion and deletion (InDel) markers were co-dominant in nature
These landraces were maintained at Indira Gandhi Krishi Viswavidyalaya, Raipur (CG), India. These genotypes were evaluated in experimental field and redundant accessions were curtailed based on morphological observations on plants and grains. Such of 190 landraces/genotypes were used in the present study to decipher genetic diversity and population structure based on InDel markers
Summary
Rice (Oryza sativa L.) is one of the most important food crops in the world and supports the requirement of staple food for almost half of the world’s population. It is cultivated in about 163.2 million ha of land and produced 751.9 million tons (in form of paddy) worldwide [1]. The genetic differentiation between indica and japonica rice provides information about adaptive evolution in plant species under the changing environments which may in turn help rice breeders for resolving partial sterility in inter-subspecies hybridization in rice [5,6]
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