Haplotype Characterization of the <i>sd1</i> Semidwarf Gene in United States Rice

Angira, Brijesh; Addison, Christopher K.; Cerioli, Tommaso; Rebong, Democrito B.; Wang, Diane; Pumplin, Nathan; Ham, Jong Hyun; Oard, James H.; Linscombe, Steven D.; Famoso, Adam N.

doi:10.3835/plantgenome2019.02.0010

“…SD1 or gibberellin 20-oxidase, a key enzyme in the gibberellin biosynthesis pathway, is located at 38.38 Mb in the Nipponbare genome assembly, directly amidst the observed strong associations with height ( Figure 6 ). The major green revolution allele semi-dwarf1 is a loss of function allele for SD1 that creates shorter plants with higher harvest indices (Angira et al . 2019).…”

Section: Discussionmentioning

confidence: 99%

“…The major green revolution allele semi-dwarf1 is a loss of function allele for SD1 that creates shorter plants with higher harvest indices (Angira et al 2019). From resequencing data analyzed in Angira et al (2019), the Global MAGIC parents include three functional SD1 haplotypes: common haplotype 2 (common in the aromatic and japonica subpopulations), common haplotype 4 (common in the aus subpopulation), and one rare haplotype in IR 4630-22-2-5-1-3 (Table S1). While our GBS dataset has no variants within SD1, we observe five haplotypes in the 24 SNPs within 300 kb: the major haplotype shared by eleven parents (with one mutation in Cypress) that is likely sd1; two similar haplotypes in Jinbubyeo/Inia Tacuari and IET 14720 that are likely linked to SD1 haplotype 2; and two divergent haplotypes in IAC 165 and IR 4630-22-2-5-1-3 that are likely linked to SD1 haplotype 4 and the rare SD1 haplotype, respectively.…”

Section: Sd1/qdty11 Has Strong Consistent Effects In the Dry Seasonmentioning

confidence: 99%

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Moyers

¹

,

Henry

²

,

Raghavan

³

et al. 2022

Preprint

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Crop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.

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“…Starting in the late 1960s, the semi-dwarf phenotype was introduced into Asian and then US breeding programs, often increasing yields in modern agronomic environments by 50% or more [32]. Though multiple alleles exist, the major source in our population is the Taichung Native 1 allele derived from an indica source [33]. 1905 -1961 1964 -1986 1990 -2013…”

Section: % Of Ld Blocks Exhibit Sweep-like Changes In Frequencymentioning

confidence: 99%

Gene disruption by structural mutations drives selection in US rice breeding over the last century

Vaughn

¹

,

Korani

²

,

Stein

³

et al. 2021

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The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion in the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.

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“…Starting in the late 1960s, the semi-dwarf phenotype was introduced into Asian and then US breeding programs, often increasing yields in modern agronomic environments by 50% or more (25). Though multiple alleles exist, the major source in our population is the Taichung Native 1 allele derived from an indica source (26).…”

Section: % Of Ld Blocks Exhibit Sweep-like Changes In Frequencymentioning

confidence: 99%

Gene disruption by structural mutations drives selection in US rice breeding over the last century

Vaughn

¹

,

Korani

²

,

Stein

³

et al. 2020

Preprint

View full text Add to dashboard Cite

The genetic basis of general plant vigor is of major interest to food producers, yet the trait is recalcitrant to genetic mapping because of the number of loci involved, their small effects, and linkage. Observations of heterosis in many crops suggests that recessive, malfunctioning versions of genes are a major cause of poor performance, yet we have little information on the mutational spectrum underlying these disruptions. To address this question, we generated a long-read assembly of a tropical japonica rice (Oryza sativa) variety, Carolina Gold, which allowed us to identify structural mutations (>50 bp) and orient them with respect to their ancestral state using the outgroup, Oryza glaberrima. Supporting prior work, we find substantial genome expansion is the sativa branch. While transposable elements (TEs) account for the largest share of size variation, the majority of events are not directly TE-mediated. Tandem duplications are the most common source of insertions and are highly enriched among 50-200bp mutations. To explore the relative impact of various mutational classes on crop fitness, we then track these structural events over the last century of US rice improvement using 101 resequenced varieties. Within this material, a pattern of temporary hybridization between medium and long-grain varieties was followed by recent divergence. During this long-term selection, structural mutations that impact gene exons have been removed at a greater rate than intronic indels and single-nucleotide mutations. These results support the use of ab initio estimates of mutational burden, based on structural data, as an orthogonal predictor in genomic selection.Significance StatementSome crop varieties have superior performance across years and environments. In hybrids, harmful mutations in one parent are masked by the ancestral alleles in the other parent, resulting in increased vigor. Unfortunately, these mutations are very difficult to identify precisely because, individually, they only have a small effect. In this study, we use long-read sequencing to characterize the entire mutational spectrum between two rice varieties. We then track these mutations through the last century of rice breeding. We show that large structural mutations in exons are selected against at a greater rate than any other mutational class. These findings illuminate the nature of deleterious alleles and will guide attempts to predict variety vigor based solely on genomic information.

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Haplotype Characterization of the sd1 Semidwarf Gene in United States Rice

Cited by 19 publications

References 29 publications

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Gene disruption by structural mutations drives selection in US rice breeding over the last century

Gene disruption by structural mutations drives selection in US rice breeding over the last century

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