Abstract
In India, rice (Oryza sativa L.) is cultivated under a variety of climatic conditions. Due to the fragility of the coastal ecosystem, rice farming in these areas has lagged behind. Salinity coupled with floods has added to this trend. Hence, to prevent genetic erosion, conserving and characterizing the coastal rice, is the need of the hour. This work accessed the genetic variation and population structure among 2,242 rice accessions originating from India’s east coast comprising Andhra Pradesh, Orissa, and Tamil Nadu, using 36 SNP markers, and have generated a core set (247 accessions) as well as a mini-core set (30 accessions) of rice germplasm. All the 36 SNP loci were biallelic and 72 alleles found with average two alleles per locus. The genetic relatedness of the total collection was inferred using the un-rooted neighbor-joining tree, which grouped all the genotypes (2,242) into three major clusters. Two groups were obtained with a core set and three groups obtained with a mini core set. The mean PIC value of total collection was 0.24, and those of the core collection and mini core collection were 0.27 and 0.32, respectively. The mean heterozygosity and gene diversity of the overall collection were 0.07 and 0.29, respectively, and the core set and mini core set revealed 0.12 and 0.34, 0.20 and 0.40 values, respectively, representing 99% of distinctiveness in the core and mini core sets. Population structure analysis showed maximum population at K = 4 for total collection and core collection. Accessions were distributed according to their population structure confirmed by PCoA and AMOVA analysis. The identified small and diverse core set panel will be useful in allele mining for biotic and abiotic traits and managing the genetic diversity of the coastal rice collection. Validation of the 36-plex SNP assay was done by comparing the genetic diversity parameters across two different rice core collections, i.e., east coast and northeast rice collection. The same set of SNP markers was found very effective in deciphering diversity at different genetic parameters in both the collections; hence, these marker sets can be utilized for core development and diversity analysis studies.
Highlights
Rice (Oryza sativa L.) is an important cereal crop which is a predominant food for over three billion people across the globe
We demonstrate the identification of a diverse core set panel from the east coast region of India comprising 247 core accessions and a mini core set of 30 accessions to enable elite gene mining for breeding and conservation and on a long-term perspective to form a panel for association studies
The Indian rice collection has remained uncharacterized at the molecular level in terms of genetic diversity and population structure
Summary
Rice (Oryza sativa L.) is an important cereal crop which is a predominant food for over three billion people across the globe. It is pivotal to comprehend the scope of genetic variation in crop germplasm and how to control it; results from molecular marker-based diversity studies should be used with caution, especially when it comes to germplasm conservation initiatives, the reason being adaptability, which plays a major role during the process of evolution and individuals’ survival in populations. As a result, it becomes ambiguous, determining whether plant selection is based on markers directly or on linked loci responsible for adaptive traits (Raybould et al, 1996)
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