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12 pages, 5420 KiB

Open AccessArticle

Deciphering the Genetic Architecture of Color Variation in Whole Grain Rice by Genome-Wide Association

by Wenjun Wang, Xianjin Qiu, Ziqi Wang, Tianyi Xie, Wenqiang Sun, Jianlong Xu, Fan Zhang and Sibin Yu

Plants 2023, 12(4), 927; https://doi.org/10.3390/plants12040927 - 17 Feb 2023

Cited by 2 | Viewed by 1470

Abstract

Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste [...] Read more.

Whole grain rice is recommended in a natural healthy diet because of its high nutritional and healthful benefits compared to polished or white rice. The whole grain contains the pericarp with many assorted colors (such as brown, red, and black) associated with taste and commercial quality. The color attributes of whole grain or brown rice are usually undesirable and need to be improved. To decipher the genetic basis of color variation in the whole grain rice, we conducted a genome-wide association analysis of three parameters of grain colors (brightness, redness, and yellowness) in a panel of 682 rice accessions. Twenty-six loci were identified for the color parameters, implying that grain color is under polygenic control. Among them, some major-effect loci were co-localized with the previously identified genes such as Rc and Rd. To eliminate the possible mask of Rc on other loci influencing grain color, we performed the association analysis in a subset of the panel that excluded the pigmented (red and black) rice. Eighteen loci or SNPs were detected to be associated with grain color in the subpopulation, many of which were not reported before. Two significant peak SNP regions on chromosomes 1 and 9 were validated using near-isogenic lines. Based on differential expression analysis of annotated genes within the SNP regions and metabolic analysis of pooled extreme samples, we found at least three annotated genes as potential candidates involved in the flavonoid metabolic pathway related to pericarp color. These results provide insights into the genetic basis of rice grain color and facilitate genomic breeding to improve appearance and commercial quality of whole grain rice. Full article

(This article belongs to the Special Issue Rice Genetics and Breeding)

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15 pages, 11385 KiB

Open AccessArticle

LG5, a Novel Allele of EUI1, Regulates Grain Size and Flag Leaf Angle in Rice

by Zhen Li, Junrong Liu, Xingyu Wang, Jing Wang, Junhua Ye, Siliang Xu, Yuanyuan Zhang, Dongxiu Hu, Mengchen Zhang, Qun Xu, Shan Wang, Yaolong Yang, Xinghua Wei, Yue Feng and Shu Wang

Plants 2023, 12(3), 675; https://doi.org/10.3390/plants12030675 - 3 Feb 2023

Viewed by 1614

Abstract

Grain size and flag leaf angle are two important traits that determining grain yield in rice. However, the mechanisms regulating these two traits remain largely unknown. In this study, a rice long grain 5 (lg5) mutant with a large flag leaf [...] Read more.

Grain size and flag leaf angle are two important traits that determining grain yield in rice. However, the mechanisms regulating these two traits remain largely unknown. In this study, a rice long grain 5 (lg5) mutant with a large flag leaf angle was identified, and map-based cloning revealed that a single base substitution followed by a 2 bp insertion in the LOC_Os05g40384 gene resulted in larger grains, a larger flag leaf angle, and higher plant height than the wild type. Sequence analysis revealed that lg5 is a novel allele of elongated uppermost internode-1 (EUI1), which encodes a cytochrome P450 protein. Functional complementation and overexpression tests showed that LG5 can rescue the bigger grain size and larger flag leaf angle in the Xiushui11 (XS) background. Knockdown of the LG5 transcription level by RNA interference resulted in elevated grain size and flag leaf angle in the Nipponbare (NIP) background. Morphological and cellular analyses suggested that LG5 regulated grain size and flag leaf angle by promoting cell expansion and cell proliferation. Our results provided new insight into the functions of EUI1 in rice, especially in regulating grain size and flag leaf angle, indicating a potential target for the improvement of rice breeding. Full article

(This article belongs to the Special Issue Rice Genetics and Breeding)

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10 pages, 1178 KiB

Open AccessArticle

Variations in Grain Traits among Local Rice Varieties Collected More Than Half-Century Ago in Indochinese Countries

by Sathya Lim, Anna Onoda, Chhourn Orn, Hiromu Iwamoto, Ryo Ishikawa, Hiroki Saito, Yutaka Sato and Takashige Ishii

Plants 2023, 12(1), 133; https://doi.org/10.3390/plants12010133 - 27 Dec 2022

Viewed by 1499

Abstract

More than half-century ago, local rice varieties were collected from Indochinese countries (Cambodia, Thailand, Laos, and Vietnam). Of these, 162 local varieties were examined for 7 grain-size traits: seed length/width/thickness, brown rice length/width/thickness, and 100-seed weight. Since these traits varied considerably, a survey [...] Read more.

More than half-century ago, local rice varieties were collected from Indochinese countries (Cambodia, Thailand, Laos, and Vietnam). Of these, 162 local varieties were examined for 7 grain-size traits: seed length/width/thickness, brown rice length/width/thickness, and 100-seed weight. Since these traits varied considerably, a survey of functional mutations was performed in the genes related to these traits. In total, 19 markers (12 InDel and 7 dCAPS markers) were used to investigate the mutations at 14 grain-size loci of GW2, GS2, qLGY3, GS3, GL3.1, TGW3, GS5, GW5, GS6, TGW6, GW6a, GLW7, GL7, and GW8. Significant allele effects were observed with six markers detecting base substitution mutations at GW2 and GS3 and insertion/deletion mutations at GS5, GW5, and GW6a, suggesting that these mutations might have affected the grain trait and caused variation among local varieties in the Indochinese countries. In addition to grain size, the hull color, grain color, and glutinosity were also examined using a survey of loss-of-function mutations at major responsible loci. Most phenotypes were reflected based on functional mutations at these loci. Since the local varieties have wide genetic variation, they are important genetic resources for future rice breeding. Full article

(This article belongs to the Special Issue Rice Genetics and Breeding)

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