The identification of grain size genes by RapMap reveals directional selection during rice domestication

Zhang, Juncheng; Zhang, Dejian; Fan, Ye‐Yang; Li, Cuicui; Xu, Pengkun; Li, Wei; Sun, Qi; Xiao-dong, Huang; Zhang, Chunyu; Wu, Linyue; Yang, Huaizhou; Wang, Shiyu; Su, Xiaomin; Li, Xingxing; Song, Yingying; Wu, Meng en; Lian, Xingming; Li, Yibo

doi:10.1038/s41467-021-25961-1

Cited by 32 publications

(24 citation statements)

References 71 publications

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“…The favorable allele for increased grain size and uniform shape is accumulated in elite germplasm because of directional selection during the domestication process (Gegas et al , 2010; Zhang et al , 2021). However, landraces that evolved from natural and human selection might still be a significant source of positive genetic diversity (Casañas et al , 2017).…”

Section: Discussionmentioning

confidence: 99%

The double round-robin population unravels the genetic architecture of grain size in barley

Shrestha

Cosenza

Inghelandt

et al. 2022

Preprint

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Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characters and observed 84 % or higher heritability across four environments. The results of the quantitative trait locus (QTL) detection indicate that the genetic architecture of grain size is more complex than reported previously. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.HighlightMulti parent population uncovered the natural allelic series across quantitative loci associated with grain size and weight that will contribute to identifying causal genes and yield improvement in barley.

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Section: Discussionmentioning

confidence: 99%

The double round-robin population unravels the genetic architecture of grain size in barley

Shrestha

Cosenza

Inghelandt

et al. 2022

Preprint

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“…In DongLanMoMi rice, several purple pericarp-related genes, such as LOC_Os02g49140, LOC_Os12g07690, and LOC_Os06g17020, were identified as candidate genes for anthocyanin biosynthesis following an analysis of F 2 progeny using the new Pair-wise Comparison Analysis for Multiple Pool-seq (PCAMP) method (Yang et al, 2019). Additionally, the recently developed Rapid multi-QTL Mapping (RapMap) method, which involves the construction of a series of F 2 gradient populations derived from multiple bi-parents with gradient phenotypes in diverse germplasms, was used to identify eight genes controlling the natural variations in rice grain length and width within 3 years (Zhang et al, 2021). The findings of the present study suggest two complementary genes regulate the green coloration of the pericarp of LM8 grains, which is in accordance with the results of earlier research.…”

Section: Discussionmentioning

confidence: 99%

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains

Han

Li²,

Qiao³

et al. 2022

Front. Plant Sci.

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The weedy rice (Oryza sativa f. spontanea) pericarp has diverse colors (e.g., purple, red, light-red, and white). However, research on pericarp colors has focused on red and purple, but not green. Unlike many other common weedy rice resources, LM8 has a green pericarp at maturity. In this study, the coloration of the LM8 pericarp was evaluated at the cellular and genetic levels. First, an examination of their ultrastructure indicated that LM8 chloroplasts were normal regarding plastid development and they contained many plastoglobules from the early immature stage to maturity. Analyses of transcriptome profiles and differentially expressed genes revealed that most chlorophyll (Chl) degradation-related genes in LM8 were expressed at lower levels than Chl a/b cycle-related genes in mature pericarps, suggesting that the green LM8 pericarp was associated with inhibited Chl degradation in intact chloroplasts. Second, the F2 generation derived from a cross between LM8 (green pericarp) and SLG (white pericarp) had a pericarp color segregation ratio of 9:3:4 (green:brown:white). The bulked segregant analysis of the F2 populations resulted in the identification of 12 known genes in the chromosome 3 and 4 hotspot regions as candidate genes related to Chl metabolism in the rice pericarp. The RNA-seq and sqRT-PCR assays indicated that the expression of the Chl a/b cycle-related structural gene DVR (encoding divinyl reductase) was sharply up-regulated. Moreover, genes encoding magnesium-chelatase subunit D and the light-harvesting Chl a/b-binding protein were transcriptionally active in the fully ripened dry pericarp. Regarding the ethylene signal transduction pathway, the CTR (encoding an ethylene-responsive protein kinase) and ERF (encoding an ethylene-responsive factor) genes expression profiles were determined. The findings of this study highlight the regulatory roles of Chl biosynthesis- and degradation-related genes influencing Chl accumulation during the maturation of the LM8 pericarp.

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“…In the process of constructing RILs population, multiple generations of arti cial and natural selection are required, which leads to the increase of partial separation ratio of this population, which is also the reason for the highest partial separation ratio of this population (Elomaa et al, 2018). It has been reported that the proportion of partial separation between molecular markers is between 24.7% and 98.9% (Zhang et al, 2021). The proportion of partial separation in this study is 0%, which is relatively low, which may be related to the population type, crop species and the selection of mapping markers.…”

Section: Discussionmentioning

confidence: 99%

QTL mapping and genetic map for the ornamental sunflower in China

Liu¹,

Shan²,

Wang³

2022

Preprint

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The quantitative trait locus (QTL) mapping and genetic map are of great significance for the ornamental sunflower in China. In this study, a total of 956.50Mbp data were obtained, the average Q30 was 93.76%, the average GC content was 42.43%, and the GC distribution of the parents and F2 population of the ornamental sunflowers was normal. At the same time, the double-end comparison efficiency of control data was 90.28%, and the enzyme digestion efficiency was 92.01%. SLAF library construction was normal. Furthermore, a total of 734,893 SLAF markers were obtained, among which 127,855 were polymorphic SLAF markers, 38,908 could be used for genetic map construction, and the effective polymorphism of the parents was 5.29%. Moreover, we constructed a total of 17 linkage groups, with 6,181 markers in the QTL mapping, the total map distance was 2,608.66cM, the marker integrity in the figure above was 99%, the proportion of double exchange was 0.05, the sequencing depth of the parents was 42.455x, and the progeny was 9.24x. The relationship of traits (plant height, stem diameter, disk diameter, number of petals, leaf number, stigma color, petal color, petiole color) and QTL mapping was closely related to show the best of ornamental effect.

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The identification of grain size genes by RapMap reveals directional selection during rice domestication

Cited by 32 publications

References 71 publications

The double round-robin population unravels the genetic architecture of grain size in barley

The double round-robin population unravels the genetic architecture of grain size in barley

Identification of candidate genes and clarification of the maintenance of the green pericarp of weedy rice grains

QTL mapping and genetic map for the ornamental sunflower in China

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