Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

Ayaad, Mohammed; Han, Zhongmin; Zheng, Kang; Hu, Gang; Abo-Yousef, Mahmoud; Sobeih, Sobeih El. S.; Xing, Yongzhong

doi:10.1016/j.jare.2020.08.001

Cited by 24 publications

(12 citation statements)

References 79 publications

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“…Appearance quality of rice determines its capability to attract consumers, and chalkiness is the main indicator of appearance quality ( Zhou et al, 2020 ; Ayaad et al, 2021 ). Seeds with high chalkiness are easily broken during milling and thus losing marketability ( Sawada et al, 2016 ).…”

Section: Discussionmentioning

confidence: 99%

Study on the Effect of Salt Stress on Yield and Grain Quality Among Different Rice Varieties

et al. 2022

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Salt is one of the main factors limiting the use of mudflats. In this study, the yield, quality, and mineral content of rice seeds under salt stress were investigated. A pot experiment was conducted with Yangyugeng2, Xudao9, and Huageng5 under 0, 17.1, 25.6, and 34.2 mM NaCl of salt concentration treatments. The results showed that salt stress can significantly decrease panicle number, grain number per panicle, 1000-grain weight and yield of rice, and the panicle number was among other things the main cause of yield loss under saline conditions. When the salt concentration is less than 34.2 mM NaCl, the salt stress increases the brown rice rate and milled rice rate, thus significant increasing head milled rice rate of salt-sensitive varieties but decreasing in salt-tolerant varieties. In addition, the grain length is more sensitive than grain width to salt stress. This study also indicates that different varieties of rice exhibit different salt tolerance under salt stress, the three rice varieties in this study, in order of salt tolerance, are Xudao9, Huageng5, and Yangyugeng2. Salt stress will increase the appearance, viscosity, degree of balance, and taste value, and decrease the hardness of rice when salt concentration is less than 17.1 mM NaCl in Yangyugeng2 and Huageng5 or 25.6 mM NaCl in Xudao9. The differences in starch pasting properties among rice varieties in this study are larger than those caused by salt stress. The uptake capacity of K, Mg, P, S, and Cu ions in the seeds of different rice varieties significantly vary, and salt stress causes significant differences in the uptake capacity of K, Na, and Cu ions in rice seeds. Rice varieties with high salt tolerance can be selected for the development and utilization of mudflats, and low concentration of salt stress will increase the rice quality, all of which are meaningful to agricultural production.

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Section: Discussionmentioning

confidence: 99%

Study on the Effect of Salt Stress on Yield and Grain Quality Among Different Rice Varieties

et al. 2022

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“…GW5 / qSW5 / GSE5 , which regulates rice GW, was cloned in 2008 ( Shomura et al, 2008 ; Weng et al, 2008 ), while some QTL analyses and GWASs found that some major QTLs for rice chalkiness were close to GW5 / qSW5 / GSE5 ( Wang et al, 2011 ; Gao et al, 2014 ; Qiu et al, 2015 , 2017 ; Ayaad et al, 2021 ). Chalk5 for rice chalkiness ( Li et al, 2014 ) and GS5 for rice grain shape ( Li et al, 2011 ), which are cloned genes, locate on chromosome 5 and are also very close to GSE5 .…”

Section: Discussionmentioning

confidence: 99%

Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape

et al. 2022

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Chalkiness is one of several major restricting factors for the improvement of rice quality. Although many chalkiness-related quantitative trait loci have been mapped, only a small number of genes have been cloned to date. In this study, the candidate gene GSE5 of a major quantitative trait locus (QTL) for rice chalkiness, qDEC5, was identified by map-based cloning. Phenotyping and haplotype analysis of proActin:GSE5 transgenic line, gse5-cr mutant, and 69 rice varieties further confirmed that GSE5 had the pleiotropic effects and regulated both chalkiness and grain shape. Genetic analysis showed GSE5 was a dominant gene for grain length and a semi-dominant gene for grain width and chalkiness. The DNA interval closely linked to GSE5 was introgressed to Zhenshan 97B (ZB) based on molecular marker-assisted selection, and the improved ZB showed lower chalkiness and longer but smaller grains, which showed that GSE5 played an important role in breeding rice varieties with high yield and good quality. Transcriptomics, proteomics, and qRT-PCR analyses showed that thirty-nine genes associated with carbon and protein metabolism are regulated by GSE5 to affect the formation of chalkiness, including some newly discovered genes, such as OsCESA9, OsHSP70, OsTPS8, OsPFK04, OsSTA1, OsERdj3A, etc. The low-chalkiness lines showed higher amino sugar and nucleotide sugar metabolism at 10 days after pollination (DAP), lower carbohydrate metabolism at 15 DAP, and lower protein metabolism at 10 and 15 DAP. With heat shock at 34/30°C, rice chalkiness increased significantly; OsDjC10 and OsSUS3 were upregulated at 6 and 12 DAP, respectively, and OsGSTL2 was downregulated at 12 DAP. Our results identified the function and pleiotropic effects of qDEC5 dissected its genetic characteristics and the expression profiles of the genes affecting the chalkiness formation, and provided a theoretical basis and application value to harmoniously pursue high yield and good quality in rice production.

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“…Grain size, in general, is controlled by several additional genes: higher expression of GW6a (Os06g0650300), and knockout of GW5 (Os05g0187500), GW6 (Os06g0623700), and GW5L (Os01g0190500) results in increased grain size (Ayaad et al, 2021;Ishimaru et al, 2013;Song et al, 2015;Tian et al, 2019;L. Zhang et al, 2020).…”

Section: Grain Number Quality Weight and Plant Structurementioning

confidence: 99%

Rice breeding in the new era: comparison of useful agronomic traits

Hernández-Soto

Echeverría-Beirute

Abdelnour-Esquivel

et al. 2021

Preprint

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Understanding agronomic traits at a genetic level enables the leveraging of this knowledge to produce crops that are more productive and resilient, have better quality and are adjusted for consumer preferences. In the last decade, rice has become a model to validate the function of specific genes, resulting in valuable but scattered information. Here, we aimed to identify particular genes in rice related to traits that can be targeted by different mutation techniques in the breeding of crops. We selected gain of function, misfunction, and specific mutations associated with phenotypes of agronomic interest. The review includes specific trait-related genes involved in domestication, stress, herbicide tolerance, pathogen resistance, grain number/quality/weight, plant structure, nitrogen use, and others. The information presented can be used for rice, other cereals, and orphan crops to achieve a superior and sustainable production in challenging farming conditions.

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Bin-based genome-wide association studies reveal superior alleles for improvement of appearance quality using a 4-way MAGIC population in rice

Abstract: Graphical abstract

Cited by 24 publications

References 79 publications

Study on the Effect of Salt Stress on Yield and Grain Quality Among Different Rice Varieties

Study on the Effect of Salt Stress on Yield and Grain Quality Among Different Rice Varieties

Identification and Pleiotropic Effect Analysis of GSE5 on Rice Chalkiness and Grain Shape

Rice breeding in the new era: comparison of useful agronomic traits

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