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Identification of QTLs for yield and grain quality traits under high night temperature using a heat multi-parent advanced generation intercrosses (MAGIC) rice population
Dissertation Abstract:
Genome-wide association studies (GWAS) were conducted using a Heat Multiparent Advanced Generation Inter-Cross (MAGIC) population to identify QTLs and significant SNP markers for yield and grain quality traits under high night temperature environments in Myanmar. Enough phenotypic variations were observed to identify significant genomic regions of different traits. In correlation study, grain yield was significantly and positively correlated with number of filled grain, plant height, chalkiness, amylose content, days to 50% flowering and maturity while positive direct effect on seed yield was contributed by number of filled grains and plant height in path coefficient analyses. These traits have also been identified as major direct contributors towards seed yield. Promising lines with multiple trait combinations were observed in this population. IR 99853-72-4-2-1 was identified as the superior rice genotypes for high night-temperature stress tolerance with high yielding characters. We detected 26 significant genomic regions on chromosome 1, 3, 5, 6, 8, 9, and 12. Four QTLs, qDF3.1, qDM3.1, qPH1.1 and qPT12.1 were displayed as consistent markers at three environments. Fifteen QTLs, qDM6.1, qDM8.1, qPH8.1, qPT1.2, qPT1.3, qFG8.1, qYLD5.2, qYLD8.2, qGL3.1, qGL8.1, qGW5.1, qAC6.1, qCHALKY6.1 and qCHALKY9.1, were identified for specific environments. Four QTLs which were mined for grain yield were qYLD5.1, qYLD5.2, q YLD8.1 and qYLD8.2. For grain yield trait, one main block on chromosome 5 and two blocks on chromosome 8 were observed through haploblock analysis. Two haplotype, ACGGGCTCG on chromosome 5 and ACCCG on chromosome 8 increased the grain yield. For number of filled grains, two haploblocks were dug on chromosome 8. The associated SNP markers were detected to co-locate with known major genes and QTLs such as OsMADS50 for days to flowering, OsMADS2 for plant height, GER2 for number of filled grains, GS3 for grain length, ADC1, sik1 and dp1 for amylose content and MUB2 for chalkiness. A number of promising candidate QTLs/genes reported in our study can be further validated. We identified several QTLs/ genes pyramided lines with acceptable yield potential and high night temperature tolerance, which are a good resource for further evaluation to release as varieties as well as for use in breeding programs.
