Blib is a multi-module simulation platform for genetics studies and intelligent breeding

Zhang, Luyan; Li, Huihui; Wang, Jiankang

doi:10.1038/s42003-022-04151-9

Cited by 4 publications

(3 citation statements)

References 39 publications

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“…Blib is a simulation platform for modelling, simulating, and predicting the genetic and breeding processes of different diploid species [ 33 ]. Our target of breeding design was to improve HR and GL.…”

Section: Methodsmentioning

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

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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%

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

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“…One QTL was located at 22.5 cM on each of the first nine chromosomes, and their genetic effects and variances were given in Table 4 . One thousand populations each of IB 1 , IB 2 and IF 2 , derived from the PIL of DHs, were generated by genetic breeding simulation platform Blib, each with a size of 200 ( Zhang et al., 2022a ). The random error variance was set to 1.…”

Section: Methodsmentioning

confidence: 99%

Combined QTL mapping on bi-parental immortalized heterozygous populations to detect the genetic architecture on heterosis

2023

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From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB1 and IB2, representing the two directions of backcrossing) and F2 (i.e., IF2) populations can be developed. These populations are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB1, IB2, and IF2) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB1 and IB2 are present, summation and subtraction are used. When IF2 and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF2 population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects.

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“…Blib is a simulation platform for modelling, simulating, and predicting the genetic and breeding process of different diploid species (Zhang et al 2022). Our target of designed breeding was to improve HR and GL.…”

Section: Breeding Simulation To Pyramid Favorite Allelesmentioning

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

Blib is a multi-module simulation platform for genetics studies and intelligent breeding

Cited by 4 publications

References 39 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

Combined QTL mapping on bi-parental immortalized heterozygous populations to detect the genetic architecture on heterosis

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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