BackgroundGenetic diversity is the main source of variability in any crop improvement program. It serves as a reservoir for identifying superior alleles controlling key agronomic and quality traits through allele mining/association mapping. Association mapping based on LD (Linkage dis-equilibrium), non-random associations between causative loci and phenotype in natural population is highly useful in dissecting out genetic basis of complex traits. For any successful association mapping program, understanding the population structure and assessing the kinship relatedness is essential before making correlation between superior alleles and traits. The present study was aimed at evaluating the genetic variation and population structure in a collection of 192 rice germplasm lines including local landraces, improved varieties and exotic lines from diverse origin.ResultsA set of 192 diverse rice germplasm lines were genotyped using 61 genome wide SSR markers to assess the molecular genetic diversity and genetic relatedness. Genotyping of 192 rice lines using 61 SSRs produced a total of 205 alleles with the PIC value of 0.756. Population structure analysis using model based and distance based approaches revealed that the germplasm lines were grouped into two distinct subgroups. AMOVA analysis has explained that 14 % of variation was due to difference between with the remaining 86 % variation may be attributed by difference within groups.ConclusionsBased on these above analysis viz., population structure and genetic relatedness, a core collection of 150 rice germplasm lines were assembled as an association mapping panel for establishing marker trait associations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-015-0062-5) contains supplementary material, which is available to authorized users.

Summary Though several genes governing various major traits have been reported in rice, their superior haplotype combinations for developing ideal variety remains elusive. In this study, haplotype analysis of 120 previously functionally characterized genes, influencing grain yield (87 genes) and grain quality (33 genes) revealed significant variations in the 3K rice genome ( RG ) panel. For selected genes, meta‐expression analysis using already available datasets along with co‐expression network provided insights at systems level. Also, we conducted candidate gene based association study for the 120 genes and identified 21 strongly associated genes governing 10‐grain yield and quality traits. We report superior haplotypes upon phenotyping the subset of 3K RG panel, SD 1 ‐H8 with haplotype frequency ( HF ) of 30.13% in 3K RG panel, MOC 1 ‐H9 ( HF : 23.08%), IPA 1 ‐H14 ( HF : 6.64%), DEP 3 ‐H2 ( HF : 5.59%), DEP 1 ‐H2 ( HF : 37.53%), SP 1 ‐H3 ( HF : 5.05%), LAX 1 ‐H5 ( HF : 1.56%), LP ‐H13 (3.64%), OSH 1 ‐H4 (5.52%), PHD 1 ‐H14 ( HF : 15.21%), AGO 7 ‐H15 ( HF : 3.33%), ROC 5 ‐H2 (31.42%), RSR 1 ‐H8 ( HF : 4.20%) and Os NAS 3 ‐H2 ( HF : 1.00%). For heading date, Ghd7 ‐H8 ( HF : 3.08%), TOB 1 ‐H10 ( HF : 4.60%) flowered early, Ghd7 ‐H14 ( HF : 42.60%), TRX 1 ‐H9 ( HF : 27.97%), Os VIL 3 ‐H14 ( HF : 1.72%) for medium duration flowering, while Ghd7 ‐H6 ( HF : 1.65%), SNB ‐H9 ( HF : 9.35%) were late flowering. GS 5 ‐H4 ( HF : 65.84%) attributed slender, GS 5 ‐H5 ( HF : 29.00%), GW 2 ‐H2 ( HF : 4.13%) were medium slender and GS 5 ‐H9 ( HF : 2.15%) for...

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Background: Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17), gall midge (GM) (Gm4, Gm8) and QTLs for drought tolerance (qDTY 1.1 and qDTY 3.1 ) through marker-assisted forward breeding (MAFB) approach. Result: Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23-26%). Out of these, three ILs viz., IL1 (Pi9+ Xa4+ xa5+ Xa21+ Bph17+ Gm8+ qDTY 1.1 + qDTY 3.1 ), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY 1.1 + qDTY 3.1 ) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY 1.1 + qDTY 3.1 ) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty. Conclusion:The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha − 1 under drought condition, without adverse effect on grain quality traits under non-stress.

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