Copy number variation at the GL7 locus contributes to grain size diversity in rice

Wang, Yuexing; Xiong, Guosheng; Hu, Jiang; Jiang, Liang; Yu, Hong; Xu, Jie; Fang, Yunxia; Zeng, Longjun; Xu, Erbo; Xu, Jing; Ye, Weijun; Meng, Xiangbing; Liu, Ruifang; Chen, Hongqi; Jing, Yanhui; Wang, Yonghong; Zhu, Xudong; Li, Jiayang; Qian, Qian

doi:10.1038/ng.3346

Cited by 491 publications

(415 citation statements)

References 25 publications

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“…For example, copy number variation in a tandem duplicated region controls rice grain size diversity, an important quality trait (Wang et al, 2015b). This region contains two copies of Grain Length on Chromosome7 (GL7) that are homologs of the Arabidopsis LONGIFOLIA gene, which regulates cell elongation.…”

Section: Contribution Of Duplicate Genes To Agronomic Traitsmentioning

confidence: 99%

“…This region contains two copies of Grain Length on Chromosome7 (GL7) that are homologs of the Arabidopsis LONGIFOLIA gene, which regulates cell elongation. Tandem duplication leads to elevated levels of GL7 expression and increased grain length (Wang et al, 2015b). Based on comparisons of wild and domesticated pepper (Capsicum annuum) species, tandem duplicate genes involved in capsaicin biosynthesis have likely contributed to the diversification of pungency in peppers (Qin et al, 2014), which may be the basis of pungency variation among domesticated pepper varieties.…”

Section: Contribution Of Duplicate Genes To Agronomic Traitsmentioning

confidence: 99%

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Evolution of Gene Duplication in Plants

2016

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Ancient duplication events and a high rate of retention of extant pairs of duplicate genes have contributed to an abundance of duplicate genes in plant genomes. These duplicates have contributed to the evolution of novel functions, such as the production of floral structures, induction of disease resistance, and adaptation to stress. Additionally, recent whole-genome duplications that have occurred in the lineages of several domesticated crop species, including wheat (Triticum aestivum), cotton (Gossypium hirsutum), and soybean (Glycine max), have contributed to important agronomic traits, such as grain quality, fruit shape, and flowering time. Therefore, understanding the mechanisms and impacts of gene duplication will be important to future studies of plants in general and of agronomically important crops in particular. In this review, we survey the current knowledge about gene duplication, including gene duplication mechanisms, the potential fates of duplicate genes, models explaining duplicate gene retention, the properties that distinguish duplicate from singleton genes, and the evolutionary impact of gene duplication.

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Section: Contribution Of Duplicate Genes To Agronomic Traitsmentioning

confidence: 99%

Section: Contribution Of Duplicate Genes To Agronomic Traitsmentioning

confidence: 99%

Evolution of Gene Duplication in Plants

2016

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“…More accessions came from China (39), Philippines (36), Madagascar (29), India (28), Senegal (24), Sri Lanka (24) and Bangladesh (15). For other countries or regions the number of accessions was fewer than eight.…”

Section: Association Mapping Panelmentioning

confidence: 99%

“…The GW1-1 and GW1-2 [5], qGRL1.1 [6], GS2 [7], GW3 and GW6 [8], qGL-4b [9], qPGWC-7 [10] qGL-7 [11], qGRL7.1 [6], gw8.1 [12], gw9.1 [13], tgw11 [14] have been fine mapped. The GW2 [15], GS3 [16], qGL-3 [17], qSW5 [18], GS5 [19], Chalk5 [20], TGW6 [21], GW6a [22], SRS1 [23], GL7/GW7 [24,25], GW8 [26] and CycT1;3 [27] have been cloned. The usefulness of some of the well characterized genes/QTL was proven in an indica population of diverse breeding lines [4].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

Fang¹,

Yingguo²,

Wu³

et al. 2018

Acta Agronomica Sinica

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Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.

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“…Comparison of wild and cultivated plants shows evidence of large-scale chromosomal structural changes [96], changes in transposable-element content and copy-number variation [97]. There is higher prevalence of recent polyploidy among major domestic crop species (34%) than among wild plant species (24%), with monocots exhibiting the most profound difference: 54% of the crops are recent polyploids versus 40% of the wild species [98].…”

Section: Plant Genomes: Crop Plants and Their Relativesmentioning

confidence: 99%

The Impact of Genetic Changes during Crop Domestication

et al. 2018

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Abstract:Humans have domesticated hundreds of plant and animal species as sources of food, fiber, forage, and tools over the past 12,000 years, with manifold effects on both human society and the genetic structure of the domesticated species. The outcomes of crop domestication were shaped by selection driven by human preferences, cultivation practices, and agricultural environments, as well as other population genetic processes flowing from the ensuing reduction in effective population size. It is obvious that any selection imposes a reduction of diversity, favoring preferred genotypes, such as nonshattering seeds or increased palatability. Furthermore, agricultural practices greatly reduced effective population sizes of crops, allowing genetic drift to alter genotype frequencies. Current advances in molecular technologies, particularly of genome sequencing, provide evidence of human selection acting on numerous loci during and after crop domestication. Population-level molecular analyses also enable us to clarify the demographic histories of the domestication process itself, which, together with expanded archaeological studies, can illuminate the origins of crops. Domesticated plant species are found in 160 taxonomic families. Approximately 2500 species have undergone some degree of domestication, and 250 species are considered to be fully domesticated. The evolutionary trajectory from wild to crop species is a complex process. Archaeological records suggest that there was a period of predomestication cultivation while humans first began the deliberate planting of wild stands that had favorable traits. Later, crops likely diversified as they were grown in new areas, sometimes beyond the climatic niche of their wild relatives. However, the speed and level of human intentionality during domestication remains a topic of active discussion. These processes led to the so-called domestication syndrome, that is, a group of traits that can arise through human preferences for ease of harvest and growth advantages under human propagation. These traits included reduced dispersal ability of seeds and fruits, changes to plant structure, and changes to plant defensive characteristics and palatability. Domestication implies the action of selective sweeps on standing genetic variation, as well as new genetic variation introduced via mutation or introgression. Furthermore, genetic bottlenecks during domestication or during founding events as crops moved away from their centers of origin may have further altered gene pools. To date, a few hundred genes and loci have been identified by classical genetic and association mapping as targets of domestication and postdomestication divergence. However, only a few of these have been characterized, and for even fewer is the role of the wild-type allele in natural populations understood. After domestication, only favorable haplotypes are retained around selected genes, which creates a genetic valley with extremely low genetic diversity. These "selective sweeps" can allow mildly deleterious...

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Copy number variation at the GL7 locus contributes to grain size diversity in rice

Cited by 491 publications

References 25 publications

Evolution of Gene Duplication in Plants

Evolution of Gene Duplication in Plants

Genome-wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm

The Impact of Genetic Changes during Crop Domestication

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