Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers
Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbr...
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| Veröffentlicht in: | Genes 2021-10, Vol.12 (11), p.1690, Article 1690 |
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| creator | Dwiningsih, Yheni Kumar, Anuj Thomas, Julie Ruiz, Charles Alkahtani, Jawaher Al-hashimi, Abdulrahman Pereira, Andy |
| description | Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of "Kaybonnet (KBNT lpa) " and "ZHE733 " named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality. |
| doi_str_mv | 10.3390/genes12111690 |
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Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of "Kaybonnet (KBNT lpa) " and "ZHE733 " named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. Continuous distributions and transgressive segregations of all the traits were observed, suggesting that the traits were quantitatively inherited. A total of twenty-eight QTLs and ninety-two candidate genes related to rice grain characteristics were identified. This genetic information is important to develop rice varieties of high quality.</description><identifier>ISSN: 2073-4425</identifier><identifier>EISSN: 2073-4425</identifier><identifier>DOI: 10.3390/genes12111690</identifier><identifier>PMID: 34828295</identifier><language>eng</language><publisher>BASEL: Mdpi</publisher><subject>Biosynthesis ; Chromosome Mapping ; Chromosomes ; Chromosomes, Plant ; Cloning ; Crosses, Genetic ; DNA, Plant - genetics ; Edible Grain - anatomy & histology ; Edible Grain - genetics ; Enzymes ; Genes ; Genetic Association Studies ; Genetic Markers ; Genetics & Heredity ; Grain size ; High-Throughput Nucleotide Sequencing ; Inbreeding ; Kinases ; Life Sciences & Biomedicine ; Oryza - anatomy & histology ; Oryza - genetics ; Oryza sativa indica ; Oryza sativa japonica ; Plants, Genetically Modified ; Polymorphism, Single Nucleotide ; Population ; Proteins ; Quantitative Trait Loci ; Rice ; Scanning electron microscopy ; Science & Technology ; Sequence Analysis, DNA ; Single-nucleotide polymorphism</subject><ispartof>Genes, 2021-10, Vol.12 (11), p.1690, Article 1690</ispartof><rights>2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 by the authors. 2021</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>6</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000723373400001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c415t-4e1bce2d227b4f4357f129c9d64c6a16ee66752728d71899fcd00c7777dab8a43</citedby><cites>FETCH-LOGICAL-c415t-4e1bce2d227b4f4357f129c9d64c6a16ee66752728d71899fcd00c7777dab8a43</cites><orcidid>0000-0003-0305-5376 ; 0000-0002-0697-9016 ; 0000-0002-0704-8803</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8625982/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8625982/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,729,782,786,887,27931,27932,39265,53798,53800</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/34828295$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Dwiningsih, Yheni</creatorcontrib><creatorcontrib>Kumar, Anuj</creatorcontrib><creatorcontrib>Thomas, Julie</creatorcontrib><creatorcontrib>Ruiz, Charles</creatorcontrib><creatorcontrib>Alkahtani, Jawaher</creatorcontrib><creatorcontrib>Al-hashimi, Abdulrahman</creatorcontrib><creatorcontrib>Pereira, Andy</creatorcontrib><title>Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers</title><title>Genes</title><addtitle>GENES-BASEL</addtitle><addtitle>Genes (Basel)</addtitle><description>Rice (Oryza sativa L.) is the primary food for half of the global population. Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of "Kaybonnet (KBNT lpa) " and "ZHE733 " named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. 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Recently, there has been increasing concern in the rice industry regarding the eating and milling quality of rice. This study was conducted to identify genetic information for grain characteristics using a recombinant inbred line (RIL) population from a japonica/indica cross based on high-throughput SNP markers and to provide a strategy for improving rice quality. The RIL population used was derived from a cross of "Kaybonnet (KBNT lpa) " and "ZHE733 " named the K/Z RIL population, consisting of 198 lines. A total of 4133 SNP markers were used to identify quantitative trait loci (QTLs) with higher resolution and to identify more accurate candidate genes. The characteristics measured included grain length (GL), grain width (GW), grain length to width ratio (RGLW), hundred grain weight (HGW), and percent chalkiness (PC). QTL analysis was performed using QTL IciMapping software. 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| subjects | Biosynthesis Chromosome Mapping Chromosomes Chromosomes, Plant Cloning Crosses, Genetic DNA, Plant - genetics Edible Grain - anatomy & histology Edible Grain - genetics Enzymes Genes Genetic Association Studies Genetic Markers Genetics & Heredity Grain size High-Throughput Nucleotide Sequencing Inbreeding Kinases Life Sciences & Biomedicine Oryza - anatomy & histology Oryza - genetics Oryza sativa indica Oryza sativa japonica Plants, Genetically Modified Polymorphism, Single Nucleotide Population Proteins Quantitative Trait Loci Rice Scanning electron microscopy Science & Technology Sequence Analysis, DNA Single-nucleotide polymorphism |
| title | Identification of Genomic Regions Controlling Chalkiness and Grain Characteristics in a Recombinant Inbred Line Rice Population Based on High-Throughput SNP Markers |
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