Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice

Wu, Yongzhen; Zhao, Shuangshuang; Li, Xianran; Zhang, Bosen; Jiang, Li‐Yun; Tang, Yanyan; Zhao, Jie; Ma, Xin; Cai, Hongwei; Sun, Chuanqing; Tan, Lubin

doi:10.1038/s41467-018-06509-2

Cited by 75 publications

(68 citation statements)

References 47 publications

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“…In the context of crop domestication and diversification, this could have led to desirable phenotypes in human-created agricultural environments. For instance, several domestication phenotypes in rice are known to be caused by gene deletions [35,[62][63][64][65][66].…”

Section: Evolution Of Circum-basmati Rice Group-specific Gene Presencmentioning

confidence: 99%

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

et al. 2020

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Background: The circum-basmati group of cultivated Asian rice (Oryza sativa) contains many iconic varieties and is widespread in the Indian subcontinent. Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group's evolutionary history is not fully resolved. To address these gaps, we use long-read nanopore sequencing and assemble the genomes of two circum-basmati rice varieties. Results: We generate two high-quality, chromosome-level reference genomes that represent the 12 chromosomes of Oryza. The assemblies show a contig N50 of 6.32 Mb and 10.53 Mb for Basmati 334 and Dom Sufid, respectively. Using our highly contiguous assemblies, we characterize structural variations segregating across circum-basmati genomes. We discover repeat expansions not observed in japonica-the rice group most closely related to circumbasmati-as well as the presence and absence variants of over 20 Mb, one of which is a circum-basmati-specific deletion of a gene regulating awn length. We further detect strong evidence of admixture between the circumbasmati and circum-aus groups. This gene flow has its greatest effect on chromosome 10, causing both structural variation and single-nucleotide polymorphism to deviate from genome-wide history. Lastly, population genomic analysis of 78 circum-basmati varieties shows three major geographically structured genetic groups: Bhutan/Nepal, India/Bangladesh/Myanmar, and Iran/Pakistan. Conclusion: The availability of high-quality reference genomes allows functional and evolutionary genomic analyses providing genome-wide evidence for gene flow between circum-aus and circum-basmati, describes the nature of circum-basmati structural variation, and reveals the presence/absence variation in this important and iconic rice variety group.

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Section: Evolution Of Circum-basmati Rice Group-specific Gene Presencmentioning

confidence: 99%

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

et al. 2020

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“…Many of these O. sativa varieties were subjected to human selection and evolved into landraces with adaptations beneficial under local conditions, but were never subjected to intensive and systematic breeding [6]. In Africa, both O. sativa and O. glaberrima accessions are grown using low-input, minimally mechanized agriculture, intended for local consumption [5] [7] [8]. The African landraces have been shown to carry several interesting traits that could empower sustainable and less demanding agricultural production.…”

Section: Introductionmentioning

confidence: 99%

CRISPR-mediated accelerated domestication of African rice landraces

et al. 2020

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African Oryza glaberrima and Oryza sativa landraces are considered valuable resources for breeding traits due to their adaptation to local environmental and soil conditions. They often possess superior resistance to endemic pests and tolerance to drought and nutrient deficiencies when compared to the "imported" high production Asian rice varieties. In contrast, "domestication traits" such as seed shattering, lodging, and seed yield are not well established in these African landraces. Therefore, the use of these African varieties for high production agriculture is limited by unpredictable yield and grain quality. We are addressing this shortcoming by developing protocols for genetically transforming African landraces to allow the use of CRISPR-Cas mediated breeding approaches. Here we use as proof of concept the cultivated African landrace Kabre to target selected known "domestication loci" and improve the agronomic potential of Kabre rice. Stable genetic transformation with CRISPR-Cas9-based vectors generated single and simultaneous multiple gene knockouts. Plants with reduced stature to diminish lodging were generated by disrupting the HTD1 gene. Furthermore, three loci shown to control seed size and/or yield (GS3, GW2 and GN1A) were targeted using a multiplex CRISPR-Cas9 construct. This resulted in mutants with significantly improved seed yield. Our study provides an example of how new breeding technologies can accelerate the development of highly productive African landrace rice varieties, an important advancement considering that Africa is a hotspot for worldwide population growth and therefore prone to food shortage. OPEN ACCESS Citation: Lacchini E, Kiegle E, Castellani M, Adam H, Jouannic S, Gregis V, et al. (2020) CRISPRmediated accelerated domestication of African rice landraces. PLoS ONE 15(3): e0229782. https://doi.

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“…ICIM has been proven to be an efficient QTL mapping method and widely used in biparental (e.g., Yin et al 2015, 2017; Wu et al 2018), 4-way-cross pure-line (e.g., Ning et al 2017), and clone F 1 and 4-way-cross F 1 populations (e.g., Ding et al 2015; Chen et al 2016). Simulation studies and application in a cowpea MAGIC population in this study validated its efficiency with 8-parental pure-line populations.…”

Section: Discussionmentioning

confidence: 99%

Genetic Mapping with Background Control for Quantitative Trait Locus (QTL) in 8-Parental Pure-Line Populations

Shi

Wang

Zhang

2019

Journal of Heredity

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Multiparental advanced generation intercross (MAGIC) populations provide abundant genetic variation for use in plant genetics and breeding. In this study, we developed a method for quantitative trait locus (QTL) detection in pure-line populations derived from 8-way crosses, based on the principles of inclusive composite interval mapping (ICIM). We considered 8 parents carrying different alleles with different effects. To estimate the 8 genotypic effects, 1-locus genetic model was first built. Then, an orthogonal linear model of phenotypes against marker variables was established to explain genetic effects of the locus. The linear model was estimated by stepwise regression and finally used for phenotype adjustment and background genetic variation control in QTL mapping. Simulation studies using 3 genetic models demonstrated that the proposed method had higher detection power, lower false discovery rate (FDR), and unbiased estimation of QTL locations compared with other methods. Marginal bias was observed in the estimation of QTL effects. An 8-parental recombinant inbred line (RIL) population previously reported in cowpea and analyzed by interval mapping (IM) was reanalyzed by ICIM and genome-wide association mapping implemented in software FarmCPU. The results indicated that ICIM identified more QTLs explaining more phenotypic variation than did IM; ICIM provided more information on the detected QTL than did FarmCPU; and most QTLs identified by IM and FarmCPU were also detected by ICIM.

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Deletions linked to PROG1 gene participate in plant architecture domestication in Asian and African rice

Cited by 75 publications

References 47 publications

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice

CRISPR-mediated accelerated domestication of African rice landraces

Genetic Mapping with Background Control for Quantitative Trait Locus (QTL) in 8-Parental Pure-Line Populations

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