Genetic diversity in representative sets of high yielding varieties of rice released in India between 1970 and 2010 was studied at molecular level employing hypervariable microsatellite markers. Of 64 rice SSR primer pairs studied, 52 showed polymorphism, when screened in 100 rice genotypes. A total of 184 alleles was identified averaging 3.63 alleles per locus. Cluster analysis clearly grouped the 100 genotypes into their respective decadal periods i.e., 1970s, 1980s, 1990s and 2000s. The trend of diversity over the decadal periods estimated based on the number of alleles (Na), allelic richness (Rs), Nei’s genetic diversity index (He), observed heterozygosity (Ho) and polymorphism information content (PIC) revealed increase of diversity over the periods in year of releasewise and longevitywise classification of rice varieties. Analysis of molecular variance (AMOVA) suggested more variation in within the decadal periods than among the decades. Pairwise comparison of population differentiation (Fst) among decadal periods showed significant difference between all the pairs except a few. Analysis of trends of appearing and disappearing alleles over decadal periods showed an increase in the appearance of alleles and decrease in disappearance in both the categories of varieties. It was obvious from the present findings, that genetic diversity was progressively on the rise in the varieties released during the decadal periods, between 1970s and 2000s.

BackgroundBasmati rice, originated in the foothills of Himalayas, commands a premium price in the domestic and international markets on account of its unique quality traits. The complex genetic nature of unique traits of Basmati as well as tedious screening methodologies involved in quality testing have been serious constraints to breeding quality Basmati. In the present study, we made an attempt to identify the genomic regions governing unique traits of Basmati rice.ResultsA total of 34 Quantitative Trait Loci (QTLs) for 16 economically important traits of Basmati rice were identified employing F2, F3 and Recombinant Inbred Line (RIL) mapping populations derived from a cross between Basmati370 (traditional Basmati) and Jaya (semi-dwarf rice). Out of which, 12 QTLs contributing to more than 15 % phenotypic variance were identified and considered as major effect QTLs. Four major effect QTLs coincide with the already known genes viz., sd1, GS3, alk1 and fgr governing plant height, grain size, alkali spreading value and aroma, respectively. For the remaining major QTLs, candidate genes were predicted as auxin response factor for filled grains, soluble starch synthase 3 for chalkiness and VQ domain containing protein for grain breadth and grain weight QTLs, based on the presence of non-synonymous single nucleotide polymorphism (SNPs) that were identified by comparing Basmati genome sequence with that of Nipponbare.ConclusionsTo the best of our knowledge, the current study is the first attempt ever made to carry out genome-wide mapping for the dissection of the genetic basis of economically important traits of Basmati rice. The promising QTLs controlling important traits in Basmati rice, identified in this study, can be used as candidates for future marker-assisted breeding.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0575-5) contains supplementary material, which is available to authorized users.

A major dwarfing region for plant height, asd1, was identified employing the next-generation sequencing-based QTL-Seq approach from a dwarf mutant and is demonstrated to be responsible for the dwarf nature with least penalty on yield in rice. The yield plateauing of modern rice is witnessed since many decades due to the narrow genetic base owing to the usage of a single recessive gene, i.e., semi-dwarf-1 (sd-1) for development of short-statured varieties throughout the world. This calls for the searching of alternate sources for short stature in rice. To this end, we made an attempt to uncover yet another, but valuable dwarfing gene employing next-generation sequencing (NGS)-based QTL-Seq approach. Here, we have identified a major QTL governing plant height on chromosome 1, i.e., alternate semi-dwarf 1 (asd1) from an F mapping population derived from a cross between a dwarf mutant, LND384, and a tall landrace, INRC10192. Fine mapping of asd1 region employing sequence-based indel markers delimited the QTL region to 67.51 Kb. The sequencing of the QTL region and gene expression analysis predicted a gene that codes for IWS1 (C-terminus family protein). Furthermore, marker-assisted introgression of the asd1 into tall landrace, INRC10192, reduced its plant height substantially while least affecting the yield and its component traits. Hence, this novel dwarfing gene, asd1, has profound implications in rice breeding.

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