Seed size is determined by the combinations of the genes controlling different seed characteristics in rice

Song, Yan; Zou, Guihua; Li, Sujuan; Wang, Hua; Liu, Heqin; Zhai, Guowei; Guo, Peng; Song, Hongmiao; Yan, Changjie; Tao, Yuezhi

doi:10.1007/s00122-011-1657-x

Cited by 84 publications

(62 citation statements)

References 32 publications

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“…The qSW5 functioned as negative regulator of grain width and weight and a deletion in qSW5 resulted in a significant increase in sink size owing to an increase in cell number in the outer glume of the rice flower and finally increased the grain width and weight [18]. The qSW5 was also reported to regulate GL, GLWR and GT [65]. However, the effects of qSW5 on PGWC and DEC have not been reported before.…”

Section: Gwas Is Effectivementioning

confidence: 91%

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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Section: Gwas Is Effectivementioning

confidence: 91%

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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“…Three qSW5 alleles have been identified, namely, Kasalath-type qSW5, indica-II type qSW5, and Nipponbare-type qSW5, which identified a 1971 bp product, 1021 bp product, 759 bp product by the molecular marker N1212del, respectively (Shomura et al, 2008;Yan et al, 2011). The gene qSW5 was cloned in a cross between Kasalath and Nipponbare varieties.…”

Section: Gene Sequence Analysismentioning

confidence: 99%

“…The intricate and complicated interactions of the genes that contribute to seed size are the principal obstacle for such gene pyramiding (Yan et al, 2011). The QTL GW8 positively regulates grain width and weight via the promotion of cell proliferation.…”

Section: Gw8 and Tgw6 Do Not Have Significant Effectsmentioning

confidence: 99%

Verification and evaluation of grain QTLs using RILs from TD70 x Kasalath in rice

et al. 2015

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ABSTRACT. Grain size is an important trait that directly influences the yield of rice. Validation and evaluation of grain genes is important in rice genetic studies and for breeding. In a population of 240 recombinant inbred lines (RILs) derived from a cross between an extra-large grain japonica variety TD70 and a small grain indica variety Kasalath, we mapped 19 QTLs controlling grain traits. These QTLs included six cloned grain genes, namely, GW2, GS3, qSW5, qGL3, GS5, and GW8. All of the alleles with the optimal effects on grain size came from TD70, the variety with extra-large grains. To verify these gene loci, we cloned and sequenced GW2, GS3, GW5 (qSW5), qGL3, GS5, GW8, and TGW6 in TD70 and Kasalath, and found several functional polymorphisms in the sequences of the genes. New functional markers for the cloned genes were designed to identify parents and RILs. The contributions of these polymorphisms to the improvement in rice grain size traits were evaluated. Our results indicate that at least six functional polymorphisms have additive effects on grain shape and that one non-functional polymorphism in TGW6 affects grain shape in TD70. The newly designed markers will be useful in further studies to identify functional grain genes. Our findings provide insight into the control of grain size in rice, and they will be of value for improving rice grain yield.

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“…Many yield-related genes have been cloned, such as GS3, GW2, GW5, GL7, Ghd7, OsSPL16, TGW6, GIF1, DTH8 and Gnla (Ashikari et al 2005;Ishimaru et al 2013;Mao et al 2010;Song et al 2007;Wang et al 2008Wang et al , 2012Wang et al , 2015Wei et al 2010;Xue et al 2008;Yan et al 2011). Some of these genes have pleiotropic effects: for example, GS3 controls both grain length and weight; Ghd7 controls grain number per spike, plant height, and heading date; GW2 controls grain width, grain weight, panicle number per plant, and heading date; and GL7 controls grain length and width.…”

Section: Introductionmentioning

confidence: 99%

Population structure and association analysis of yield and grain quality traits in hybrid rice primal parental lines

et al. 2016

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To make advances in rice molecular design breeding, it is important to understand the genetic background and phenotypes of the parental lines, to known superior allele of the breeding material. In this study, 34 pairs of insertion-deletion (InDel) markers were used to analyze the differentiation of indica-japonica properties in 277 primal parental lines of hybrid rice that are used in China and abroad. The genetic diversity and population structure were assessed with simple sequence repeat (SSR) markers. We also evaluated the association between SSR markers and seven yield traits and four grainquality traits of 256 indica rice lines. The main results are as follows. (1) Euphytica (2016) 212:261-273 DOI 10.1007/s10681-016-1766 eight for grain width, eight for grain length/width ratio, one for thousand grain weight, one for amylose content, two for gel consistency, one for gelatinization temperature and one for total protein content. (3) Among those loci, 16 markers were closely linked to previously identified genes. Superior allele carrier lines and allele effects were also analyzed. Our results provided the population structure and indica-japonica properties for parent matching, and the marker-trait association will also be useful for molecular design breeding.

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Seed size is determined by the combinations of the genes controlling different seed characteristics in rice

Cited by 84 publications

References 32 publications

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

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

Verification and evaluation of grain QTLs using RILs from TD70 x Kasalath in rice

Population structure and association analysis of yield and grain quality traits in hybrid rice primal parental lines

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