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Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice
Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recover...
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Published in: | Frontiers in plant science 2023-03, Vol.14, p.1133115-1133115 |
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creator | Kumari, Anita Sharma, Divya Sharma, Priya Wang, Chaoxin Verma, Vibha Patil, Arun Imran, Md Singh, Madan Pal Kumar, Kuldeep Paritosh, Kumar Caragea, Doina Kapoor, Sanjay Chandel, Girish Grover, Anil Jagadish, S V Krishna Katiyar-Agarwal, Surekha Agarwal, Manu |
description | Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes,
and
, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits. |
doi_str_mv | 10.3389/fpls.2023.1133115 |
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and
, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.</description><identifier>ISSN: 1664-462X</identifier><identifier>EISSN: 1664-462X</identifier><identifier>DOI: 10.3389/fpls.2023.1133115</identifier><identifier>PMID: 36968399</identifier><language>eng</language><publisher>Switzerland: Frontiers Media S.A</publisher><subject>grain chalkiness ; granule bound starch synthase I ; haplo-pheno analysis ; haplotype ; meta-QTL analysis ; Plant Science ; starch metabolism</subject><ispartof>Frontiers in plant science, 2023-03, Vol.14, p.1133115-1133115</ispartof><rights>Copyright © 2023 Kumari, Sharma, Sharma, Sahil, Wang, Verma, Patil, Imran, Singh, Kumar, Paritosh, Caragea, Kapoor, Chandel, Grover, Jagadish, Katiyar-Agarwal and Agarwal.</rights><rights>Copyright © 2023 Kumari, Sharma, Sharma, Sahil, Wang, Verma, Patil, Imran, Singh, Kumar, Paritosh, Caragea, Kapoor, Chandel, Grover, Jagadish, Katiyar-Agarwal and Agarwal 2023 Kumari, Sharma, Sharma, Sahil, Wang, Verma, Patil, Imran, Singh, Kumar, Paritosh, Caragea, Kapoor, Chandel, Grover, Jagadish, Katiyar-Agarwal and Agarwal</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c466t-766b52c6669c3f0396480f352366fd083f588b1ec53b91ac4994656aa60c77053</citedby><cites>FETCH-LOGICAL-c466t-766b52c6669c3f0396480f352366fd083f588b1ec53b91ac4994656aa60c77053</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10031497/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10031497/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/36968399$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Kumari, Anita</creatorcontrib><creatorcontrib>Sharma, Divya</creatorcontrib><creatorcontrib>Sharma, Priya</creatorcontrib><creatorcontrib>Wang, Chaoxin</creatorcontrib><creatorcontrib>Verma, Vibha</creatorcontrib><creatorcontrib>Patil, Arun</creatorcontrib><creatorcontrib>Imran, Md</creatorcontrib><creatorcontrib>Singh, Madan Pal</creatorcontrib><creatorcontrib>Kumar, Kuldeep</creatorcontrib><creatorcontrib>Paritosh, Kumar</creatorcontrib><creatorcontrib>Caragea, Doina</creatorcontrib><creatorcontrib>Kapoor, Sanjay</creatorcontrib><creatorcontrib>Chandel, Girish</creatorcontrib><creatorcontrib>Grover, Anil</creatorcontrib><creatorcontrib>Jagadish, S V Krishna</creatorcontrib><creatorcontrib>Katiyar-Agarwal, Surekha</creatorcontrib><creatorcontrib>Agarwal, Manu</creatorcontrib><creatorcontrib>Sahil</creatorcontrib><creatorcontrib>Sahil</creatorcontrib><title>Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice</title><title>Frontiers in plant science</title><addtitle>Front Plant Sci</addtitle><description>Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes,
and
, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.</description><subject>grain chalkiness</subject><subject>granule bound starch synthase I</subject><subject>haplo-pheno analysis</subject><subject>haplotype</subject><subject>meta-QTL analysis</subject><subject>Plant Science</subject><subject>starch metabolism</subject><issn>1664-462X</issn><issn>1664-462X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNpVkstu1DAUhiMEolXpA7BBXrLJYMeXxCuEKi6VBiGkIrGzTpyTiYsTB9tpNe_AQ5Nhhqr15tjH__nsxVcUrxndcN7od_3s06aiFd8wxjlj8llxzpQSpVDVz-eP9mfFZUq3dF2SUq3rl8UZV1o1XOvz4s9XzFB-v9kSmDoywOxDOQ84hfUMfp9cIhHvEDxJy4zRhXgM5f2MxIaxdRNkF6ZEIKVgHWTsyL3LA_HhnuwiuInYAfwvN2FKZJk6XAluN5CM4wqEvEQkayg6i6-KFz34hJenelH8-PTx5upLuf32-frqw7a0Qqlc1kq1srJKKW15T7lWoqE9lxVXqu9ow3vZNC1DK3mrGVihtVBSAShq65pKflFcH7ldgFszRzdC3JsAzvxrhLgzELOzHs2K6gGElD2lQqFosNKaWoudAMERV9b7I2te2hE7i1OO4J9An95MbjC7cGcYpZwJXa-EtydCDL8XTNmMLln0HiYMSzJVrVlNm0qoNcqOURtDShH7h3cYNQcrzMEKc7DCnKxYZ948_uDDxH8H-F_JwLb2</recordid><startdate>20230308</startdate><enddate>20230308</enddate><creator>Kumari, Anita</creator><creator>Sharma, Divya</creator><creator>Sharma, Priya</creator><creator>Wang, Chaoxin</creator><creator>Verma, Vibha</creator><creator>Patil, Arun</creator><creator>Imran, Md</creator><creator>Singh, Madan Pal</creator><creator>Kumar, Kuldeep</creator><creator>Paritosh, Kumar</creator><creator>Caragea, Doina</creator><creator>Kapoor, Sanjay</creator><creator>Chandel, Girish</creator><creator>Grover, Anil</creator><creator>Jagadish, S V Krishna</creator><creator>Katiyar-Agarwal, Surekha</creator><creator>Agarwal, Manu</creator><general>Frontiers Media S.A</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20230308</creationdate><title>Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice</title><author>Kumari, Anita ; Sharma, Divya ; Sharma, Priya ; Wang, Chaoxin ; Verma, Vibha ; Patil, Arun ; Imran, Md ; Singh, Madan Pal ; Kumar, Kuldeep ; Paritosh, Kumar ; Caragea, Doina ; Kapoor, Sanjay ; Chandel, Girish ; Grover, Anil ; Jagadish, S V Krishna ; Katiyar-Agarwal, Surekha ; Agarwal, Manu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c466t-766b52c6669c3f0396480f352366fd083f588b1ec53b91ac4994656aa60c77053</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>grain chalkiness</topic><topic>granule bound starch synthase I</topic><topic>haplo-pheno analysis</topic><topic>haplotype</topic><topic>meta-QTL analysis</topic><topic>Plant Science</topic><topic>starch metabolism</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Kumari, Anita</creatorcontrib><creatorcontrib>Sharma, Divya</creatorcontrib><creatorcontrib>Sharma, Priya</creatorcontrib><creatorcontrib>Wang, Chaoxin</creatorcontrib><creatorcontrib>Verma, Vibha</creatorcontrib><creatorcontrib>Patil, Arun</creatorcontrib><creatorcontrib>Imran, Md</creatorcontrib><creatorcontrib>Singh, Madan Pal</creatorcontrib><creatorcontrib>Kumar, Kuldeep</creatorcontrib><creatorcontrib>Paritosh, Kumar</creatorcontrib><creatorcontrib>Caragea, Doina</creatorcontrib><creatorcontrib>Kapoor, Sanjay</creatorcontrib><creatorcontrib>Chandel, Girish</creatorcontrib><creatorcontrib>Grover, Anil</creatorcontrib><creatorcontrib>Jagadish, S V Krishna</creatorcontrib><creatorcontrib>Katiyar-Agarwal, Surekha</creatorcontrib><creatorcontrib>Agarwal, Manu</creatorcontrib><creatorcontrib>Sahil</creatorcontrib><creatorcontrib>Sahil</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>Frontiers in plant science</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Kumari, Anita</au><au>Sharma, Divya</au><au>Sharma, Priya</au><au>Wang, Chaoxin</au><au>Verma, Vibha</au><au>Patil, Arun</au><au>Imran, Md</au><au>Singh, Madan Pal</au><au>Kumar, Kuldeep</au><au>Paritosh, Kumar</au><au>Caragea, Doina</au><au>Kapoor, Sanjay</au><au>Chandel, Girish</au><au>Grover, Anil</au><au>Jagadish, S V Krishna</au><au>Katiyar-Agarwal, Surekha</au><au>Agarwal, Manu</au><aucorp>Sahil</aucorp><aucorp>Sahil</aucorp><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice</atitle><jtitle>Frontiers in plant science</jtitle><addtitle>Front Plant Sci</addtitle><date>2023-03-08</date><risdate>2023</risdate><volume>14</volume><spage>1133115</spage><epage>1133115</epage><pages>1133115-1133115</pages><issn>1664-462X</issn><eissn>1664-462X</eissn><abstract>Chalk, an undesirable grain quality trait in rice, is primarily formed due to high temperatures during the grain-filling process. Owing to the disordered starch granule structure, air spaces and low amylose content, chalky grains are easily breakable during milling thereby lowering head rice recovery and its market price. Availability of multiple QTLs associated with grain chalkiness and associated attributes, provided us an opportunity to perform a meta-analysis and identify candidate genes and their alleles contributing to enhanced grain quality. From the 403 previously reported QTLs, 64 Meta-QTLs encompassing 5262 non-redundant genes were identified. MQTL analysis reduced the genetic and physical intervals and nearly 73% meta-QTLs were narrower than 5cM and 2Mb, revealing the hotspot genomic regions. By investigating expression profiles of 5262 genes in previously published datasets, 49 candidate genes were shortlisted on the basis of their differential regulation in at least two of the datasets. We identified non-synonymous allelic variations and haplotypes in 39 candidate genes across the 3K rice genome panel. Further, we phenotyped a subset panel of 60 rice accessions by exposing them to high temperature stress under natural field conditions over two Rabi cropping seasons. Haplo-pheno analysis uncovered haplotype combinations of two starch synthesis genes,
and
, significantly contributing towards the formation of grain chalk in rice. We, therefore, report not only markers and pre-breeding material, but also propose superior haplotype combinations which can be introduced using either marker-assisted breeding or CRISPR-Cas based prime editing to generate elite rice varieties with low grain chalkiness and high HRY traits.</abstract><cop>Switzerland</cop><pub>Frontiers Media S.A</pub><pmid>36968399</pmid><doi>10.3389/fpls.2023.1133115</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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subjects | grain chalkiness granule bound starch synthase I haplo-pheno analysis haplotype meta-QTL analysis Plant Science starch metabolism |
title | Meta-QTL and haplo-pheno analysis reveal superior haplotype combinations associated with low grain chalkiness under high temperature in rice |
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