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"Exon capture"

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"Exon capture"

Research Articles
Identification of Rice Mutants with Altered Grain Alkali Digestion Trait
HyunJung Kim, Ralph Vin B. Imatong, Thomas H. Tai
Plant Breed. Biotech. 2020;8(1):19-27.   Published online March 1, 2020
DOI: https://doi.org/10.9787/PBB.2020.8.1.19

Gelatinization temperature (GT) is an important component of eating and cooking quality (ECQ) of rice. While direct measurement of GT is cumbersome, the alkali spreading value (ASV) test is a robust method commonly used to rapidly identify different GT types. In this study, we employed a modified ASV assay to screen a population of chemically-induced rice (cv. Kitaake) mutants (n = 405). Two mutant families, KDS-1623B and KDS-1824B, with significantly lower ASV (higher GT type) than wild type Kitaake (low GT type) were isolated. A nonsynonymous homozygous mutation in the isoamylase-type starch debranching enzyme gene ISA1 was identified in KDS-1623B. The mutation (G2709T) is predicted to change a valine at position 354 to a leucine in the α-amylase catalytic domain of ISA1. This result is consistent with the shrunken endosperm exhibited by KDS-1623B grains and the replacement of starch with phytoglycogen in isa1 (sugary-1) mutants. The altered ASV trait in KDS-1824B appears to be controlled by a single recessive mutation; however, the causal genetic lesion remains to be determined. These mutants will be useful resources for elucidating the complex nature of starch metabolism and its influence on ECQ of rice.

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  • Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
    Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
    G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
  • Efficient identification of palatability-related genes using QTL mapping in rice breeding
    Yoon-Hee Jang, Jae-Ryoung Park, Eun-Gyeong Kim, Rahmatullah Jan, Saleem Asif, Muhammad Farooq, Dan-Dan Zhao, Kyung-Min Kim
    Molecular Breeding.2023;[Epub]     CrossRef
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Identifying a Candidate Mutation Underlying a Reduced Cuticle Wax Mutant of Rice Using Targeted Exon Capture and Sequencing
HyunJung Kim, Thomas H. Tai
Plant Breed. Biotech. 2019;7(1):1-11.   Published online March 1, 2019
DOI: https://doi.org/10.9787/PBB.2019.7.1.1

Aerial surfaces of terrestrial plants are protected from the uncontrolled loss of water and gas by the cuticle, a membrane of fatty acid polymers on the outer surface of epidermal cells. Composed of cutin and waxes, the cuticle protects against a wide range of external stresses and has an important role in plant development and reproduction. Plants with reduced cuticular waxes often exhibit glossy, bright green leaves, which in rice are only observed in the presence of water adhesion. In this study, a wet leaf/glossy (wlg) mutant KDS-2249D was subjected to targeted exon capture and sequencing to identify candidate mutations. A single nonsynonymous, homozygous mutation was found in the KDS-2249D mutant. The mutation (G1080A) is predicted to change a tryptophan at position 360 to a stop codon in the Glossy1-like-1/wax crystal-sparse leaf 2 gene. This mutation completely co-segregated with the wlg phenotype in an F2 mapping population (n = 435) and the KDS-2249D mutant exhibited a 40–50% decrease in total wax and significant increase in membrane permeability. This mutant will be useful for studies examining the role of cuticle waxes in protecting rice plants from environmental stresses.

Citations

Citations to this article as recorded by  
  • Identification of a novel mutant allele of the LIKE EARLY STARVATION 1 gene in rice (Oryza sativa L.) using QTL-seq
    Kyu-Chan Shim, HyunJung Kim, Mi-Ra Yoon, Sung-Ho Na, Sa-Eun Park, Sang-Nag Ahn, Thomas H Tai, J Holland
    G3: Genes, Genomes, Genetics.2026;[Epub]     CrossRef
  • Comparative Genomic Analysis and Functional Identification of CER1 and CER3 Homologs in Rice Wax Synthesis
    Nesma E. E. Youssif, Bowen Yang, Haodong Huang, Mohamed Hamdy Amar, Mohamed Ezzat, Mohammad Belal, Sanaa A. M. Zaghlool, Huayan Zhao, Dong Fu, Shiyou Lü
    Biology.2026; 15(2): 166.     CrossRef
  • Identification and bioinformatic characterization of rare variants of Rhododendron canescens architecture genes
    Lav K. Yadav, H. Dayton Wilde
    Euphytica.2022;[Epub]     CrossRef
  • Identification of Rice Mutants with Altered Grain Alkali Digestion Trait
    HyunJung Kim, Ralph Vin B. Imatong, Thomas H. Tai
    Plant Breeding and Biotechnology.2020; 8(1): 19.     CrossRef
  • Deciphering the Novel Role of AtMIN7 in Cuticle Formation and Defense against the Bacterial Pathogen Infection
    Zhenzhen Zhao, Xianpeng Yang, Shiyou Lü, Jiangbo Fan, Stephen Opiyo, Piao Yang, Jack Mangold, David Mackey, Ye Xia
    International Journal of Molecular Sciences.2020; 21(15): 5547.     CrossRef
  • 12 View
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  • 5 Crossref