Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Fujino, Kenji; Kawahara, Yoshihiro; Koyanagi, Kanako O.; Shirasawa, Kenta

doi:10.1270/jsbbs.20089

Cited by 11 publications

(4 citation statements)

References 28 publications

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“…The analysis implements a clustering method similar to that in the population program ADMIXTURE (Alexander et al, 2009). The genomic data for Japanese, Chinese and U.S. weedy rice and Japanese cultivated rice, which were obtained in the previous studies (Arai‐Kichise et al, 2011; Arai‐Kichise et al, 2014; Fujino et al, 2021; Imaizumi et al, 2021; Li et al, 2017; Qiu et al, 2017; Tanaka et al, 2020; Wei et al, 2016; Xu et al, 2011), were retrieved from the DRA/DDBJ repository. The raw paired‐end reads were first trimmed with Trimmomatic version 0.38 (Bolger et al, 2014) with the parameters “ILLUMINACLIP:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:10:20 MINLEN:30”.…”

Section: Methodsmentioning

confidence: 99%

Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

2022

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Hybridization is a widespread phenomenon in plants and is a pathway for the evolution of adaptive traits. However, this process may also affect the persistence of combinations of adaptive alleles evolved through natural selection when hybridization occurs between adapted and non-adapted populations. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. In this study, we explored the influence of hybridization on the conservation of combinations of adaptive alleles by evaluating the natural variation in and the genetic structure of genomic regions associated with seed dormancy. Based on sequence variation in the genomic regions associated with seed dormancy, we revealed that hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait that were observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, the hybrid-derived weedy rice strains had deeper seed dormancy than their parental weedy rice strains. This study suggests that hybridization between weedy rice (having adaptive allelic combinations for seed dormancy) and cultivated rice (having non-adaptive combinations) generates weedy rice strains that express deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and non-adapted populations seems to be reinforcing the trajectory towards the evolution of adaptive traits.

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Section: Methodsmentioning

confidence: 99%

Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

2022

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“…Within 60 years in rice breeding programs in Hokkaido, from the start of the programs in 1915, awn was completely lost on both phenotype and genotype on RAE1 and RAE2. During rice breeding programs in Hokkaido, genomic changes have been characterized (Fujino et al 2015(Fujino et al , 2021Shinada et al 2014). Our ndings of rae1 gene ows and multiple rae2 alleles clearly demonstrated that rice breeding programs could generate genetic diversity among self-pollinating plant.…”

Section: Discussionmentioning

confidence: 71%

Control of awn length in rice breeding programs in Hokkaido

et al. 2022

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Understanding genetic diversity is a primary goal of the molecular evolution of the genes. Awn length is a well-documented phenotype among domestication traits in rice, from long to short awn. In addition, awnlessness is favor for current rice farmers. Here, we identi ed the genetic basis of awn length during rice breeding programs in Hokkaido. We found variation of awn length ranging from 0.0 to 37.6 mm.Varieties with a short-awn or awnlessness have been selected under rice breeding programs. Genetic analysis on awn length identi ed that RAE1 and RAE2 on chromosomes 4 and 8, respectively, accounted for awning. These genes were well known to be signi cant during Asian rice domestication. Sequence variations of the genes would clarify the molecular evolution of the genes on awn length. Firstly, the lossof-function allele in RAE1, rae1, was selected for short awn length. Then, alleles on RAE2, RAE2-H01 to RAE2-H04, were targeted for the selection of short-awn or awnlessness. The selections on awnlessness phenotype could diversify these alleles on the genes, RAE1 and RAE2, exhibiting the variation of awn length.

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“…Two accessions (JRC21 and JRC40) were excluded from this study due to the contradictions in genotype and degree of nucleotide polymorphism. Fourth, rice varieties from Hokkaido were used, denoted as 20V, accessible in the DDBJ BioProject database under accession numbers DRA008447, DRA006623, and DRA006604, respectively (Fujino et al 2015(Fujino et al , 2018(Fujino et al , 2021Fujino and Ikegaya 2020). The genome sequences of all varieties were assembled from high-throughput sequencing short reads.…”

Section: Genome Sequencesmentioning

confidence: 99%

Physical mapping of qDTH3 for heading date reveals the evolutionary history of cultivated rice

Ikegaya

Shirasawa

Fujino

2022

Preprint

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Crop breeding programs can improve traits associated with desirable phenotypic characteristics to different local environmental conditions. In rice, such improvements were achieved depending on genetic diversity among local populations. Here, we examined whether differences in traits of elite varieties are due to genetic differences and from what the genetic differences are derived. Previously, we identified one quantitative trait locus associated with heading date, i.e., the quantitative trait locus for days to heading on chromosome 3 (qDTH3). Using 592 plants of the F2 generation, fine mapping narrowed the qDTH3 locus down to a 158-kb region of the corresponding rice reference genome. Based on the genome sequences of a 656-kb region including the qDTH3 locus among four Oryza species populations, we propose the historic evolutionary process of cultivated rice, considering nucleotide polymorphisms and intrapopulation recombination. Phenotypic differences in qDTH3 in elite varieties may be derived from a different lineage split from the ancestor.

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Translation of continuous artificial selection on phenotype into genotype during rice breeding programs

Cited by 11 publications

References 28 publications

Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Hybrid‐derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy

Control of awn length in rice breeding programs in Hokkaido

Physical mapping of qDTH3 for heading date reveals the evolutionary history of cultivated rice

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