Genetic control of grain appearance quality in rice

Zhao, Dongsheng; Zhang, Changquan; Li, Qianfeng; Liu, Qiaoquan

doi:10.1016/j.biotechadv.2022.108014

Cited by 41 publications

(40 citation statements)

References 271 publications

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“…These traits showed extensive genetic variation and varied according to MAGIC populations (DC1, DC2 and 8way) with different GBs, suggesting that phenotypic variation largely depended on the parents and their recombination in MAGIC populations. Rice grain type has high heritability and was mainly affected by genotype (Zhao et al, 2022). However, chalkiness was caused by the deposition of starch and storage proteins in the endosperm, which was controlled by a complex genetic mechanism and sensitive to environment (Ishimaru et al, 2020;Liu et al, 2022).…”

Section: Phenotypic Variation Of Appearance Quality Of Rice In Magic ...mentioning

confidence: 99%

Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice

et al. 2022

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Many QTL have been identified for grain appearance quality by linkage analysis (LA) in bi-parental mapping populations and by genome-wide association study (GWAS) in natural populations in rice. However, few of the well characterized genes/QTL have been successfully applied in molecular rice breeding due to genetic background (GB) and environment effects on QTL expression and deficiency of favorable alleles. In this study, GWAS and LA were performed to identify QTL for five grain appearance quality-related traits using three multi-parent advanced generation inter-cross (MAGIC) populations. A total of 22 QTL on chromosomes 1-3, 5-8 were identified by GWAS for five traits in DC1, DC2 and 8way, and four combined populations DC12 (DC1+DC2), DC18 (DC1+8way), DC28 (DC2+8way) and DC128 (DC1+DC2+8way). And a total of 42 QTL were identified on all 12 chromosomes except 10 by LA in the three single populations. Among 20 QTL identified by GWAS in DC1, DC2 and 8way, 10, four and three QTL were commonly detected in DC18, DC28, and DC128, respectively. Similarly, among 42 QTL detected by LA in the three populations, four, one and two QTL were commonly detected in DC18, DC28, and DC128, respectively. There was no QTL mapped together in DC12 by both two mapping methods, indicating that GB could greatly affect the mapping results, and it was easier to map the common QTL among populations with similar GB. The 8way population was more powerful for QTL mapping than the DC1, DC2 and various combined populations. Compared with GWAS, LA can not only identify large-effect QTL, but also identify minor-effect ones. Among 11 QTL simultaneously detected by the two methods in different GBs and environments, eight QTL corresponded to known genes, including AqGL3b and AqGLWR3a for GL and GLWR, AqGW5a, AqGLWR5, AqDEC5 and AqPGWC5 for GW, GLWR, DEC and PGWC, and AqDEC6b and AqPGWC6b for DEC and PGWC, respectively. AqGL7, AqGL3c/AqGLWR3b, AqDEC6a/AqPGWC6a, and AqPGWC7 were newly identified and their candidate genes were analyzed and inferred. It was discussed to further improve grain appearance quality through designed QTL pyramiding strategy based on the stable QTL identified in the MAGIC populations.

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Section: Phenotypic Variation Of Appearance Quality Of Rice In Magic ...mentioning

confidence: 99%

Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice

et al. 2022

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“…Grain shape and size are important appearance quality of rice, which are one of the most direct characteristics for consumers and influence the market value of grain products. In general, long and slender grains have higher competitive market value, which is preferred by consumers in most regions of the world [ 1 , 2 , 3 , 4 ]. Grain size is also a major determinant of grain weight, one of the three yield components (number of panicles per plant, number of grains per panicle, and grain weight).…”

Section: Introductionmentioning

confidence: 99%

“…Some elite alleles of these QTLs have been tried for targeted improvement of rice by genome editing system [ 3 , 35 , 36 , 37 ]. However, much more effort is needed to fully understand the regulatory mechanisms of grain shape and size [ 4 , 38 , 39 ]. Moreover, the identification of more genes could provide the flexibility needed to design various rice grain shapes [ 4 ].…”

Section: Introductionmentioning

confidence: 99%

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Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background

Wang

Yingguo

et al. 2022

Plants

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Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NILZS97, NILMY46, and another rice cultivar carrying the OsPUB3MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NILZS97 and NILMY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well.

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“…

Rice (Oryza sativa L.) is a staple food for more than half of the world's population, and thus increasing rice yield is an important way to ensure food security. Grain size, including grain length, width, and thickness, is a direct determinant of grain weight and yield in rice and an important target trait for breeding selection (Xing et al 2010;Zuo et al 2014;Zhao et al 2022). In recent years, numerous genes related to grain size have been identified.

…”

mentioning

confidence: 99%

Wide Grain 3, a GRAS Protein, Interacts with DLT to Regulate Grain Size and Brassinosteroid Signaling in Rice

Chen

et al. 2022

Rice

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Background: Grain size is a direct determinant of grain weight and yield in rice; however, the genetic and molecular mechanisms determining grain size remain largely unknown. Findings: We identified a mutant, wide grain 3 (wg3), which exhibited significantly increased grain width and 1000-grain weight. Cytological analysis showed that WG3 regulates grain size by affecting cell proliferation. MutMap-based gene cloning and a transgenic experiment demonstrated that WG3 encodes a GRAS protein. Moreover, we found that WG3 directly interacts with DWARF AND LOW-TILLERING (DLT), a previously reported GRAS protein, and a genetic experiment demonstrated that WG3 and DLT function in a common pathway to regulate grain size. Additionally, a brassinosteroid (BR) sensitivity test suggested that WG3 has a positive role in BR signaling in rice. Collectively, our results reveal a new genetic and molecular mechanism for the regulation of grain size in rice by the WG3-DLT complex, and highlight the important functions of the GRAS protein complex in plants. Conclusion: WG3 functions directly in regulating grain size and BR signaling in rice.

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Genetic control of grain appearance quality in rice

Cited by 41 publications

References 271 publications

Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice

Genetic background- and environment-independent QTL and candidate gene identification of appearance quality in three MAGIC populations of rice

Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background

Wide Grain 3, a GRAS Protein, Interacts with DLT to Regulate Grain Size and Brassinosteroid Signaling in Rice

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