Robustification of Linear Regression and Its Application in Genome-Wide Association Studies

Alamin, Md.; Sultana, Most. Humaira; Xu, Haiming; Mollah, Md. Nurul Haque

doi:10.3389/fgene.2020.00549

Cited by 2 publications

(3 citation statements)

References 35 publications

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“…QTL mapping was conducted in each environment separately, as well as the BLUP values across environments. The REG method proposed by Alamin et al [ 29 ] was also adopted for QTL mapping in each environment as a comparison, which only output position and LOD score of each scanning position. As the two populations can also be viewed as CSSLs, we also used the RSTEP-LRT-ADD method in the CSL function of QTL IciMapping [ 30 ], which conducted QTL mapping in each environment separately as well as the means across environments.…”

Section: Methodsmentioning

confidence: 99%

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Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

Emelin,

Qiu,

Fan

et al. 2024

BMC Plant Biol

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Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits, both determine farmers’ final profit. More than one population under multiple environments may provide valuable information for breeding selection on these MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our major tasks were (1) to provide a set of reciprocal introgression lines (composed of two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test the mapping effects of different methods by using MQ-GS correlation dissection as sample case; (3) to perform genetic and breeding simulation on pyramiding favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci on average for MQ-GS traits. Notably, 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful resources for rice molecular breeding.

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Section: Methodsmentioning

confidence: 99%

Section: Qtl Mapping For Grain Shape and Milling Quality Traits In Th...mentioning

confidence: 99%

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

Emelin,

Qiu,

Fan

et al. 2024

BMC Plant Biol

Self Cite

View full text Add to dashboard Cite

show abstract

“…QTL mapping was conducted in each environment separately, as well as the BLUP values across environments. REG method proposed in Alamin et al (Alamin et al 2020) was also adopted for QTL mapping in each environment as a comparison, which only output position and LOD score of each scanning position. As the two populations can also be viewed as CSSLs, we also used RSTEP-LRT-ADD method in CSL function for QTL mapping (Wang et al 2007a; Wang et al 2007b), which conducted QTL mapping in each environment separately as well as the means across environments.…”

Section: Phenotypic Data Analysismentioning

confidence: 99%

Identification and designed QTL breeding of reliable QTLs for milling quality and grain shape in the reciprocal introgression lines in rice

Emelin

Qiu

Fan

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

Milling quality (MQ) and grain shape (GS) of rice (Oryza sativa L.) are correlated traits and both determining farmers’ final profit. More than one population under multiple environments may provide valuable information for breeding selection on this MQ-GS correlations. However, suitable analytical methods for reciprocal introgression lines with linkage map for this kind of correlation remains unclear. In this study, our objectives were (1) to provide a set of reciprocal introgression lines (composed by two BC2RIL populations) suitable for mapping by linkage mapping using markers/bins with physical positions; (2) to test mapping effect by MQ-GS correlation dissection by different mapping methods; (3) to perform genetic and breeding simulation to pyramid favorite alleles of QTLs for representative MQ-GS traits. Finally, with four analysis methods and data collected under five environments, we identified about 28.4 loci in average for MQ-GS traits. It’s notable that 52.3% of these loci were commonly detected by different methods and eight loci were novel. There were also nine regions harboring loci for different MQ-GS traits which may be underlying the MQ-GS correlations. Background independent (BI) loci were also found for each MQ and GS trait. All these information may provide useful data for rice molecular breeding.

show abstract

Robustification of Linear Regression and Its Application in Genome-Wide Association Studies

Cited by 2 publications

References 35 publications

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

Identification of reliable QTLs and designed QTL breeding for grain shape and milling quality in the reciprocal introgression lines in rice

Identification and designed QTL breeding of reliable QTLs for milling quality and grain shape in the reciprocal introgression lines in rice

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