Loading…
Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study
The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of...
Saved in:
| Published in: | Plants (Basel) 2024-01, Vol.13 (1), p.134 |
|---|---|
| Main Authors: | , , , , , , , , |
| Format: | Article |
| Language: | English |
| Subjects: | |
| Citations: | Items that this one cites |
| Online Access: | Get full text |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| cited_by | |
|---|---|
| cites | cdi_FETCH-LOGICAL-c513t-2ddbb3f9cc93abccfb212719f2d20a13c4709bf0ea4defd7784110b60e6435573 |
| container_end_page | |
| container_issue | 1 |
| container_start_page | 134 |
| container_title | Plants (Basel) |
| container_volume | 13 |
| creator | Ding, Xiaowen Shi, Jubin Gui, Jinxin Zhou, Huang Yan, Yuntao Zhu, Xiaoya Xie, Binying Liu, Xionglun He, Jiwai |
| description | The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only
was detected repeatedly two times. The candidate gene analysis showed that
,
and
were the candidate genes for
,
and
, respectively. The haplotype (Hap) analysis revealed that Hap1 of
, Hap1 and 3 of
and Hap2 and 5 of
are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of
is a favorable allele for the germination percentage; Hap3 of
is an elite allele for seed germination; and Hap5 of
is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice. |
| doi_str_mv | 10.3390/plants13010134 |
| format | article |
| fullrecord | <record><control><sourceid>gale_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_4b099951f3774537bccbcc8f6d971773</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A779347158</galeid><doaj_id>oai_doaj_org_article_4b099951f3774537bccbcc8f6d971773</doaj_id><sourcerecordid>A779347158</sourcerecordid><originalsourceid>FETCH-LOGICAL-c513t-2ddbb3f9cc93abccfb212719f2d20a13c4709bf0ea4defd7784110b60e6435573</originalsourceid><addsrcrecordid>eNpdkk1vEzEQhlcIRKvSK0e0Ehc4pPhjN16fUFRBiRQENEVIXCyvPd44StaL7a3af98JCVWDbcmW_bzvyDNTFK8pueBckg_DRvc5UU4oobx6VpwyxvhEiEo8f3I-Kc5TWhMcDS46fVmc8IYRVlXstPh97Q2USwBbfo8hxzH50Jc_RjT2WWd_C-VN1D6Xi2B8-VUPg--7Mq9iGLtVeQV92MLkl7dQzlJCBCWoX-bR3r8qXji9SXB-2M-Kn58_3Vx-mSy-Xc0vZ4uJqSnPE2Zt23InjZFct8a4llEmqHTMMqIpN5UgsnUEdGXBWSGailLSTglMK17Xgp8V872vDXqthui3Ot6roL36exFip3TM3mxAVS2RUtbUcUxMzQWGw9W4qZWCCsHR6-PeaxjbLVgDfY56c2R6_NL7lerCraJENEQyig7vDg4x_BkhZbX1ycAGSwVhTIpJLFVN9sHe_oeuwxh7zNWOYoI3kjVIXeypTuMPfO-wStrgtLD1JvTgPN7PhJC8ErTeCd4fCZDJcJc7Paak5svrY_ZgbmJIKYJ7_Colatdj6rjHUPDmaYIe8X8dxR8A62bMnw</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2912738928</pqid></control><display><type>article</type><title>Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study</title><source>PubMed Central (Open Access)</source><source>Publicly Available Content Database</source><creator>Ding, Xiaowen ; Shi, Jubin ; Gui, Jinxin ; Zhou, Huang ; Yan, Yuntao ; Zhu, Xiaoya ; Xie, Binying ; Liu, Xionglun ; He, Jiwai</creator><creatorcontrib>Ding, Xiaowen ; Shi, Jubin ; Gui, Jinxin ; Zhou, Huang ; Yan, Yuntao ; Zhu, Xiaoya ; Xie, Binying ; Liu, Xionglun ; He, Jiwai</creatorcontrib><description>The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only
was detected repeatedly two times. The candidate gene analysis showed that
,
and
were the candidate genes for
,
and
, respectively. The haplotype (Hap) analysis revealed that Hap1 of
, Hap1 and 3 of
and Hap2 and 5 of
are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of
is a favorable allele for the germination percentage; Hap3 of
is an elite allele for seed germination; and Hap5 of
is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.</description><identifier>ISSN: 2223-7747</identifier><identifier>EISSN: 2223-7747</identifier><identifier>DOI: 10.3390/plants13010134</identifier><identifier>PMID: 38202442</identifier><language>eng</language><publisher>Switzerland: MDPI AG</publisher><subject>Alleles ; Amino acids ; Biosynthesis ; Crop production ; Frequency distribution ; Gene mapping ; Genes ; Genetic aspects ; Genetic control ; Genome-wide association studies ; Genomes ; Germination ; Germplasm ; Growth ; GWAS ; haplotype ; Haplotypes ; Identification and classification ; Phenotypes ; Physiological aspects ; Population studies ; Proteins ; protrusion percentage ; QTL ; Quantitative trait loci ; Rice ; Seed germination ; Seeds ; Signal transduction</subject><ispartof>Plants (Basel), 2024-01, Vol.13 (1), p.134</ispartof><rights>COPYRIGHT 2024 MDPI AG</rights><rights>2024 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>2024 by the authors. 2024</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><cites>FETCH-LOGICAL-c513t-2ddbb3f9cc93abccfb212719f2d20a13c4709bf0ea4defd7784110b60e6435573</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2912738928/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2912738928?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25753,27924,27925,37012,37013,44590,53791,53793,74998</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/38202442$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Ding, Xiaowen</creatorcontrib><creatorcontrib>Shi, Jubin</creatorcontrib><creatorcontrib>Gui, Jinxin</creatorcontrib><creatorcontrib>Zhou, Huang</creatorcontrib><creatorcontrib>Yan, Yuntao</creatorcontrib><creatorcontrib>Zhu, Xiaoya</creatorcontrib><creatorcontrib>Xie, Binying</creatorcontrib><creatorcontrib>Liu, Xionglun</creatorcontrib><creatorcontrib>He, Jiwai</creatorcontrib><title>Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study</title><title>Plants (Basel)</title><addtitle>Plants (Basel)</addtitle><description>The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only
was detected repeatedly two times. The candidate gene analysis showed that
,
and
were the candidate genes for
,
and
, respectively. The haplotype (Hap) analysis revealed that Hap1 of
, Hap1 and 3 of
and Hap2 and 5 of
are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of
is a favorable allele for the germination percentage; Hap3 of
is an elite allele for seed germination; and Hap5 of
is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.</description><subject>Alleles</subject><subject>Amino acids</subject><subject>Biosynthesis</subject><subject>Crop production</subject><subject>Frequency distribution</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic control</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Germination</subject><subject>Germplasm</subject><subject>Growth</subject><subject>GWAS</subject><subject>haplotype</subject><subject>Haplotypes</subject><subject>Identification and classification</subject><subject>Phenotypes</subject><subject>Physiological aspects</subject><subject>Population studies</subject><subject>Proteins</subject><subject>protrusion percentage</subject><subject>QTL</subject><subject>Quantitative trait loci</subject><subject>Rice</subject><subject>Seed germination</subject><subject>Seeds</subject><subject>Signal transduction</subject><issn>2223-7747</issn><issn>2223-7747</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2024</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNpdkk1vEzEQhlcIRKvSK0e0Ehc4pPhjN16fUFRBiRQENEVIXCyvPd44StaL7a3af98JCVWDbcmW_bzvyDNTFK8pueBckg_DRvc5UU4oobx6VpwyxvhEiEo8f3I-Kc5TWhMcDS46fVmc8IYRVlXstPh97Q2USwBbfo8hxzH50Jc_RjT2WWd_C-VN1D6Xi2B8-VUPg--7Mq9iGLtVeQV92MLkl7dQzlJCBCWoX-bR3r8qXji9SXB-2M-Kn58_3Vx-mSy-Xc0vZ4uJqSnPE2Zt23InjZFct8a4llEmqHTMMqIpN5UgsnUEdGXBWSGailLSTglMK17Xgp8V872vDXqthui3Ot6roL36exFip3TM3mxAVS2RUtbUcUxMzQWGw9W4qZWCCsHR6-PeaxjbLVgDfY56c2R6_NL7lerCraJENEQyig7vDg4x_BkhZbX1ycAGSwVhTIpJLFVN9sHe_oeuwxh7zNWOYoI3kjVIXeypTuMPfO-wStrgtLD1JvTgPN7PhJC8ErTeCd4fCZDJcJc7Paak5svrY_ZgbmJIKYJ7_Colatdj6rjHUPDmaYIe8X8dxR8A62bMnw</recordid><startdate>20240101</startdate><enddate>20240101</enddate><creator>Ding, Xiaowen</creator><creator>Shi, Jubin</creator><creator>Gui, Jinxin</creator><creator>Zhou, Huang</creator><creator>Yan, Yuntao</creator><creator>Zhu, Xiaoya</creator><creator>Xie, Binying</creator><creator>Liu, Xionglun</creator><creator>He, Jiwai</creator><general>MDPI AG</general><general>MDPI</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7X2</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>LK8</scope><scope>M0K</scope><scope>M7P</scope><scope>P64</scope><scope>PATMY</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20240101</creationdate><title>Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study</title><author>Ding, Xiaowen ; Shi, Jubin ; Gui, Jinxin ; Zhou, Huang ; Yan, Yuntao ; Zhu, Xiaoya ; Xie, Binying ; Liu, Xionglun ; He, Jiwai</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c513t-2ddbb3f9cc93abccfb212719f2d20a13c4709bf0ea4defd7784110b60e6435573</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2024</creationdate><topic>Alleles</topic><topic>Amino acids</topic><topic>Biosynthesis</topic><topic>Crop production</topic><topic>Frequency distribution</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic control</topic><topic>Genome-wide association studies</topic><topic>Genomes</topic><topic>Germination</topic><topic>Germplasm</topic><topic>Growth</topic><topic>GWAS</topic><topic>haplotype</topic><topic>Haplotypes</topic><topic>Identification and classification</topic><topic>Phenotypes</topic><topic>Physiological aspects</topic><topic>Population studies</topic><topic>Proteins</topic><topic>protrusion percentage</topic><topic>QTL</topic><topic>Quantitative trait loci</topic><topic>Rice</topic><topic>Seed germination</topic><topic>Seeds</topic><topic>Signal transduction</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ding, Xiaowen</creatorcontrib><creatorcontrib>Shi, Jubin</creatorcontrib><creatorcontrib>Gui, Jinxin</creatorcontrib><creatorcontrib>Zhou, Huang</creatorcontrib><creatorcontrib>Yan, Yuntao</creatorcontrib><creatorcontrib>Zhu, Xiaoya</creatorcontrib><creatorcontrib>Xie, Binying</creatorcontrib><creatorcontrib>Liu, Xionglun</creatorcontrib><creatorcontrib>He, Jiwai</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Agricultural Science Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni)</collection><collection>ProQuest Central</collection><collection>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>AUTh Library subscriptions: ProQuest Central</collection><collection>ProQuest Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection (Proquest) (PQ_SDU_P3)</collection><collection>ProQuest Biological Science Collection</collection><collection>Agriculture Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science Database</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Environmental Science Collection</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>Plants (Basel)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Ding, Xiaowen</au><au>Shi, Jubin</au><au>Gui, Jinxin</au><au>Zhou, Huang</au><au>Yan, Yuntao</au><au>Zhu, Xiaoya</au><au>Xie, Binying</au><au>Liu, Xionglun</au><au>He, Jiwai</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study</atitle><jtitle>Plants (Basel)</jtitle><addtitle>Plants (Basel)</addtitle><date>2024-01-01</date><risdate>2024</risdate><volume>13</volume><issue>1</issue><spage>134</spage><pages>134-</pages><issn>2223-7747</issn><eissn>2223-7747</eissn><abstract>The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only
was detected repeatedly two times. The candidate gene analysis showed that
,
and
were the candidate genes for
,
and
, respectively. The haplotype (Hap) analysis revealed that Hap1 of
, Hap1 and 3 of
and Hap2 and 5 of
are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of
is a favorable allele for the germination percentage; Hap3 of
is an elite allele for seed germination; and Hap5 of
is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.</abstract><cop>Switzerland</cop><pub>MDPI AG</pub><pmid>38202442</pmid><doi>10.3390/plants13010134</doi><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 2223-7747 |
| ispartof | Plants (Basel), 2024-01, Vol.13 (1), p.134 |
| issn | 2223-7747 2223-7747 |
| language | eng |
| recordid | cdi_doaj_primary_oai_doaj_org_article_4b099951f3774537bccbcc8f6d971773 |
| source | PubMed Central (Open Access); Publicly Available Content Database |
| subjects | Alleles Amino acids Biosynthesis Crop production Frequency distribution Gene mapping Genes Genetic aspects Genetic control Genome-wide association studies Genomes Germination Germplasm Growth GWAS haplotype Haplotypes Identification and classification Phenotypes Physiological aspects Population studies Proteins protrusion percentage QTL Quantitative trait loci Rice Seed germination Seeds Signal transduction |
| title | Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study |
| url | http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-08T00%3A06%3A46IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Rice%20Seed%20Protrusion%20Quantitative%20Trait%20Loci%20Mapping%20through%20Genome-Wide%20Association%20Study&rft.jtitle=Plants%20(Basel)&rft.au=Ding,%20Xiaowen&rft.date=2024-01-01&rft.volume=13&rft.issue=1&rft.spage=134&rft.pages=134-&rft.issn=2223-7747&rft.eissn=2223-7747&rft_id=info:doi/10.3390/plants13010134&rft_dat=%3Cgale_doaj_%3EA779347158%3C/gale_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c513t-2ddbb3f9cc93abccfb212719f2d20a13c4709bf0ea4defd7784110b60e6435573%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2912738928&rft_id=info:pmid/38202442&rft_galeid=A779347158&rfr_iscdi=true |