QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

Dang, Xiaojing; Liu, Erbao; Yh, Liang; Liu, Qiangming; Breria, Caleb M.; Hong, Delin

doi:10.3389/fpls.2016.01188

Cited by 29 publications

(28 citation statements)

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“…3 ). This fact further confirmed that directional evolution for the allele size has occurred in rice [ 24 , 31 ]. We also observed that the SSR alleles tended to decrease in size from the low-latitude subpopulations (SP3 and SP4, 17–23゜N) to the high-latitude subpopulations (the other five subpopulations, 30–39゜N); this behaviour may be explained by the emergence of mutations or changes in the mutation rate causing a change in the allele size in rice [ 43 , 44 ].…”

Section: Discussionsupporting

confidence: 73%

“…The second was the neighbour-joining method, which was carried out using MEGA version 5.0 based on Nei’s genetic distance [ 30 ]. The computations followed the same approach as those described in [ 31 ]. The coefficient of genetic differentiation ( F ST ) [ 32 ] was calculated to measure the fixation of different alleles in different subpopulations using Arlequin version 3.0 [ 33 ].…”

Section: Methodsmentioning

confidence: 99%

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Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

et al. 2017

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BackgroundPoor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.ResultsIn this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses. The seven common loci detected by the two analytical methods were located on chromosomes 2, 3 (2), 7, 8 and 12 (2) and explained 7.24~22.28% of the variance. Of these 7 association loci, five markers linked to GP were newly detected: RM5340 on Chr2, RM5480 and RM148 on Chr3, RM1235 on Chr8, and RM5479 on Chr12.ConclusionsFive marker-GP association loci were newly detected using both the GLM and MLM analytical methods. Elite allele RM505-170 bp had the highest average phenotypic effect on increasing the GP, and the typical carrier variety was ‘Maozitou’. Based on the distribution of the elite alleles among the carrier varieties, the top 10 parental combinations for improving the GP in rice via cross-breeding were predicted.Electronic supplementary materialThe online version of this article (10.1186/s12863-017-0559-6) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 73%

Section: Methodsmentioning

confidence: 99%

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

et al. 2017

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“…Association mapping (AM) based on linkage disequilibrium (LD) has been frequently used to search for more than two alleles at a gene locus or additional gene loci and explore the natural genomic diversity at a population level (Zhu et al, 2008 ; Brachi et al, 2011 ; Weigel, 2012 ). AM has been widely applied to exploit favorable marker alleles in rice for many traits, including yield traits (Garris et al, 2005 ; Agrama et al, 2007 ; Huang et al, 2010 , 2011 ; Zhao et al, 2011 ; Li et al, 2012 ; Vanniarajan et al, 2012 ; Dang et al, 2015 ; Yang et al, 2015 ; McCouch et al, 2016 ), quality traits (Borba et al, 2010 ; Huang et al, 2010 ; Jin et al, 2010 ; Feng et al, 2016 ), resistance traits (Famoso et al, 2011 ; Jia et al, 2012 , 2016 ; Cui et al, 2013 , seed vigor traits Cui et al, 2013 ; Dang et al, 2014 ; Rebolledo et al, 2015 ; Phung et al, 2016 ), and outcrossing traits (Yan et al, 2009 ; Huang et al, 2010 ; Dang et al, 2016 ). Although several studies on associations between markers and the PEL trait in rice have been reported (Begum et al, 2015 ; Crowell et al, 2016 ), no significant association has been detected between PEL and molecular markers.…”

Section: Introductionmentioning

confidence: 99%

Favorable Marker Alleles for Panicle Exsertion Length in Rice (Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method

et al. 2017

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The panicle exsertion length (PEL) in rice (Oryza sativa L.) is an important trait for hybrid seed production. We investigated the PEL in a chromosome segment substitution line (CSSL) population consisting of 66 lines and a natural population composed of 540 varieties. In the CSSL population, a total of seven QTLs for PEL were detected across two environments. The percentage of phenotypic variance explained (PVE) ranged from 10.22 to 50.18%, and the additive effect ranged from −1.77 to 6.47 cm. Among the seven QTLs, qPEL10.2 had the largest PVE, 44.05 and 50.18%, with an additive effect of 5.91 and 6.47 cm in 2015 and in 2016, respectively. In the natural population, 13 SSR marker loci were detected that were associated with PEL in all four environments, with the PVE ranging from 1.20 to 6.26%. Among the 13 loci, 7 were novel. The RM5746-170 bp allele had the largest phenotypic effect (5.11 cm), and the typical carrier variety was Qiaobinghuang. An RM5620-RM6100 region harboring the EUI2 locus on chromosome 10 was detected in both populations. The sequencing results showed that the accessions with a shorter PEL contained the A base, while the accessions with a longer PEL contained the G base at the 1,475 bp location of the EUI2 gene.

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“…The tested materials were 542 rice accessions 1 [46]; 121 of which were from Vietnam (Indica), while the remaining accessions were from China (Tej). These accessions range from 17°N to 54°N and 102°E to135°E, crossing 37°latitude from the north to the south and 33°longitude from the east to west (Additional file 6: Table S2).…”

Section: Plant Materialsmentioning

confidence: 99%

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

Ali

Eltahawy

et al. 2020

BMC Genet

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Background: Wet direct-seeded rice is a possible alternative to conventional puddled transplanted rice; the former uses less water and reduces labor requirements. Improving seed reserve utilization efficiency (SRUE) is a key factor in facilitating the application of this technology. However, the QTLs controlling this trait are poorly investigated. In this study, a genome-wide association study (GWAS) was conducted using a natural population composed of 542 accessions of rice (Oryza sativa L.) which were genotyped using 266 SSR markers. Large phenotypic variations in SRUE were found in the studied population. Results: The average SRUE over 542 accessions across two years (2016 and 2017) was 0.52 mg.mg − 1 , ranging from 0.22 mg.mg-1 to 0.93 mg.mg − 1 , with a coefficient of variation of 22.66%. Overall, 2879 marker alleles were detected in the population by 266 pairs of SSR markers, indicating a large genetic variation existing in the population. Using general linear model method, 13 SSR marker loci associated with SRUE were detected and two (RM7309 and RM434) of the 13 loci, were also detected using mixed linear model analyses, with percentage of phenotypic variation explained (PVE) greater than 5% across two years. The 13 association loci (P < 0.01) were located on all chromosomes except chromosome 11, with PVE ranging from 5.05% (RM5158 on chromosome 5) to 12% (RM297 on chromosome 1). Association loci RM7309 on chromosome 6 and RM434 on chromosome 9 revealed by both models were detected in both years. Twenty-three favorable alleles were identified with phenotypic effect values (PEV) ranging from 0.10 mg.mg − 1 (RM7309-135 bp on chromosome 9) to 0.45 mg.mg − 1 (RM297-180 bp on chromosome 2). RM297-180 bp showed the largest phenotypic effect value (0.44 mg.mg − 1 in 2016 and 0.45 mg.mg − 1 in 2017) with 6.72% of the accessions carrying this allele and the typical carrier accession was Manyedao, followed by RM297-175 bp (0.43 mg.mg − 1 in 2016 and 0.44 mg.mg − 1 in 2017). Conclusion: Nine novel association loci for SRUE were identified, compared with previous studies. The optimal parental combinations for pyramiding more favorable alleles for SRUE were selected and could be used for breeding rice accessions suitable for wet direct seeding in the future.

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QTL Detection and Elite Alleles Mining for Stigma Traits in Oryza sativa by Association Mapping

Cited by 29 publications

References 80 publications

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

Favorable Marker Alleles for Panicle Exsertion Length in Rice (Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method

Mining of favorable alleles for seed reserve utilization efficiency in Oryza sativa by means of association mapping

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