Factors affecting head rice yield and chalkiness in indica rice

Zhou, Lean; Liang, Shanshan; Ponce, Kimberly; Marundon, Severino; Ye, Guoyou; Zhao, Xiaojing

doi:10.1016/j.fcr.2014.12.004

Cited by 115 publications

(123 citation statements)

References 38 publications

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“…The positive correlations of GW with chalkiness were also reported in previous studies (Li et al, 2014; Qiu et al, 2015; Zhao et al, 2015; Zhou et al, 2015). This phenomenon could be partially explained by tightly linked QTL or QTL pleiotropy for GW and chalkiness.…”

Section: Discussionsupporting

confidence: 86%

New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses

et al. 2017

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Appearance and milling quality are two crucial properties of rice grains affecting its market acceptability. Understanding the genetic base of rice grain quality could considerably improve the high quality breeding. Here, we carried out an association analysis to identify QTL affecting nine rice grain appearance and milling quality traits using a diverse panel of 258 accessions selected from 3K Rice Genome Project and evaluated in two environments Sanya and Shenzhen. Genome-wide association analyses using 22,488 high quality SNPs identified 72 QTL affecting the nine traits. Combined gene-based association and haplotype analyses plus functional annotation allowed us to shortlist 19 candidate genes for seven important QTL regions affecting the grain quality traits, including two cloned genes (GS3 and TUD), two fine mapped QTL (qGRL7.1 and qPGWC7) and three newly identified QTL (qGL3.4, qGW1.1, and qGW10.2). The most likely candidate gene(s) for each important QTL were also discussed. This research demonstrated the superior power to shortlist candidate genes affecting complex phenotypes by the strategy of combined GWAS, gene-based association and haplotype analyses. The identified candidate genes provided valuable sources for future functional characterization and genetic improvement of rice appearance and milling quality.

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Section: Discussionsupporting

confidence: 86%

New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses

et al. 2017

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“…Zhou et al. () also reported a 10% higher head rice yield in the dry season than in the wet season. This apparent effect of the environment on head rice yield is likely attributable to temperature and solar radiation (Deng et al., ; Liu et al., ), which are higher in the dry season in Senegal at the crop's late reproductive stage.…”

Section: Discussionmentioning

confidence: 91%

Variations in agronomic and grain quality traits of rice grown under irrigated lowland conditions in West Africa

Graham‐Acquaah

Saito

Traoré³

et al. 2018

Food Science & Nutrition

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Rice breeding in West Africa has been largely skewed toward yield enhancement and stress tolerance. This has led to the variable grain quality of locally produced rice in the region. This study sought to assess variations in the agronomic and grain quality traits of some rice varieties grown in this region, with a view to identifying sources of high grain yield and quality that could serve as potential donors in their breeding programs. Forty‐five varieties were grown under irrigated conditions in Benin and Senegal with two trials in each country. There were wide variations in agronomic and grain quality traits among the varieties across the trials. Cluster analysis using paddy yield, head rice yield, and chalkiness revealed that 68% of the total variation could be explained by five varietal groupings. One group comprising seven varieties (Afrihikari, BG90‐2, IR64, Sahel 108, WAT311‐WAS‐B‐B‐23‐7‐1, WAT339‐TGR‐5‐2, and WITA 10) had high head rice yield and low chalkiness. Of the varieties in this group, Sahel 108 had the highest paddy yield in three of the four trials. IR64 and Afrihikari had intermediate and low amylose content, respectively, with the rest being high‐amylose varieties. Another group of varieties consisting of B6144F‐MR‐6‐0‐0, C74, IR31851‐96‐2‐3‐2‐1, ITA222, Jaya, Sahel 305, WITA 1, and WITA 2 had high paddy yield but poor head rice yield and chalkiness. The use of materials from these two groups of varieties could accelerate breeding for high yielding rice varieties with better grain quality for local production in West Africa.

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“…Next, to primer InDel 14 amplification products were consistent with the phenotype at 84%, and finally, RM21938 at 76%. Chalkiness is very susceptible to environmental conditions such as temperature, fertilizer, and humidity, which might be an important reason why only a few associations were identified using published markers [17]. Here, we identified for grain chalkiness using 7 InDel markers and SSR marker Techniques polymorphism genotyping in 50 varieties.…”

Section: Discussionmentioning

confidence: 99%

Identifying the Grain Chalkiness Gene Using Molecular Marker Techniques in Rice (<i>Oryza sativa</i> L.)

Lang¹,

Giang²,

et al. 2017

ILNS

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Chalkiness is a major constraint on rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. In this study, we conducted grain chalkiness gene identification using co-dominant insertion/deletion (INDEL) markers and SSR marker combination on 50 different varieties. The application results in 7 InDel markers and SSR marker on chromosome 7 were recorded. Three primers, InDel 5, InDel 14 and RM21938, associated with grain chalkiness. For the InDel 5 primer, the amplification product was 100%. Use of primer InDel 5 in detection and evaluation of genotype to the chalkiness trait of rice grain on 50 rice varieties indicated the suitability level with phenotypic evaluation was 86% and the unsuitability level was 14%. For the InDel 14 primer, the amplification products were 100%. The suitability with phenotypic assessment was 84% and the unsuitability was 16%. For the RM21938 primer, the amplification product was 94%. The suitability with phenotypic assessment was 76% and the unsuitability was 24%. Thirteen of the selected varieties had grain chalkiness gene both InDel 5, InDel 14 and RM21938. Total 13 varieties were detected from InDel 5, InDel 14 and RM12938 primer combinations also showed high efficiency of the InDel technique in identifying chalkiness gene in rice grain. A cluster analysis was performed and a dendrogram was constructed which evinced the nature of phylogenetic classification among the genotypes of the varieties. These markers could be used for developing quality of rice in breeding program.

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Factors affecting head rice yield and chalkiness in indica rice

Cited by 115 publications

References 38 publications

New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses

New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses

Variations in agronomic and grain quality traits of rice grown under irrigated lowland conditions in West Africa

Identifying the Grain Chalkiness Gene Using Molecular Marker Techniques in Rice (<i>Oryza sativa</i> L.)

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