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. 2022 Jul 26;11(15):1930.
doi: 10.3390/plants11151930.

Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica- japonica Hybridization in Rice

Jayanth Kallugudi  1 , Vikram Jeet Singh  1 , Kunnumal Kurungara Vinod  1 , Subbaiyan Gopala Krishnan  1 , Shekharappa Nandakumar  1 , Brijesh Kumar Dixit  1 , Ranjith Kumar Ellur  1 , Haritha Bollinedi  1 , Mariappan Nagarajan  2 , Amit Kumar  3 , Mridul Chakraborti  4 , Rakesh Kumar Seth  5 , Tapan Kumar Mondal  6 , Prolay Kumar Bhowmick  1 , Ashok Kumar Singh  1
Affiliations

Population Dynamics of Wide Compatibility System and Evaluation of Intersubspecific Hybrids by indica- japonica Hybridization in Rice

Jayanth Kallugudi et al. Plants (Basel). .

Abstract

The exploitation of heterosis through intersubspecific hybridisation between indica and japonica has been a major breeding target in rice, but is marred by the cross incompatibility between the genomes. Wide compatibility (WC) is a triallelic system at the S5 locus on chromosome 6 that ensures the specificity of hybridisation within and between indica and japonica. The S5n allele that favours intercrossing is sparsely distributed in the rice gene pool and therefore warrants identification of diverse WC sources to develop superior intersubspecific hybrids. In this study, we have identified several novel WC sources through the marker-assisted screening of a large set of 950 rice genotypes. Seventeen percent of the genotypes carried S5n, which fell into two subpopulations. The WC genotypes showed wide phenotypic and genotypic variability, including both indica and japonica lines. Based on phenotypic performance, the WC varieties were grouped into three clusters. A subset of 41 WC varieties was used to develop 164 hybrids, of which WC/japonica hybrids showed relative superiority over WC/indica hybrids. The multilocation evaluation of hybrids indicated that hybrids derived from WC varieties, such as IRG137, IRG143, OYR128, and IRGC10658, were higher yielding across all the three different locations. Most of the hybrids showed the stability of performance across locations. The identified diverse set of wide compatible varieties (WCVs) can be used in the development of intersubspecific hybrids and also for parental line development in hybrid rice breeding.

Keywords: S5n; indica-japonica; inter sub-species hybridization; wide compatible varieties.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Frequency distribution of different alleles of S5 locus viz., S5-n, S5-i and S5-j in the set of 950 rice genotypes. TPJ, tropical japonica; IRG, international rice germplasm; GP, local germplasm.
Figure 2
Figure 2
Representative gel images showing the amplification profile of functional markers for different alleles of S5 locus viz., S5-n, S5-i and S5-j in the 967 lines. (a) Screening for S5-n allele using S5-InDel primer; (b) screening for S5-i allele using S5-ELSP; (c) screening for S5-j allele using S5-JASP1.
Figure 3
Figure 3
Dendrogram showing the morphological diversity among 92 WCVs based on morphological traits.
Figure 4
Figure 4
The maximum Δk estimate indicates the presence of two subpopulations among the wide compatible varieties.
Figure 5
Figure 5
Representation of genetic distance among wide compatible varieties.
Figure 6
Figure 6
Combined biplots for multilocation performance wide compatible hybrids based on GGE biplot analysis on the most significant NPT related traits.
See this image and copyright information in PMC

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