{"id":{"repo_id":"uiuc","oai_identifier":"oai:www.ideals.illinois.edu:2142/105226"},"canonical_url":"https://search.dev.ndltd.org/etd/uiuc/oai:www.ideals.illinois.edu:2142/105226","repository":{"repo_id":"uiuc","name":"University of Illinois - Urbana-Champaign","base_url":"https://www.ideals.illinois.edu/oai-pmh"},"display":{"title":"Identification of causal mutations of grain chalkiness in rice EMS populations via mapping-by-sequencing","abstract":"Abnormal endosperm development of rice (Oryza sativa L.) often produces a chalky phenotype, which strongly affects appearance, quality and grain weight. Although many enzymes and related regulators associated with endosperm chalk have been identified, many other related factors remain largely unknown. Here we describe a genetic screen for mutants with increased chalkiness from a mutagenized population of the rice mega-variety, IR64. From an initial population of 9853 M2 families, 41 were identified with heritable chalky phenotypes, which were also often associated with reductions in grain size. The M3848 mutant was unique in displaying a strong chalky phenotype but no change in seed size and was characterized in greater detail. The M3848 mutant has an opaque endosperm and abnormal starch granules and is inherited as a single locus recessive. Representative of the opaque/floury phenotype, grains of M3848 showed a higher grain percent chalkiness in comparison with that of IR64 Wild Type (IR64_WT). The contents of amylose in M3848 significantly decreased, while short chain amylopectins significantly increased and its physicochemical properties were also altered. DNA sequencing was used to identify single nucleotide polymorphisms (SNPs) highly enriched among plants displaying the M3848 mutant phenotype compared to siblings with normal phenotypes. Although these analyses did not clearly discover the causal mutation for the M3848 mutation, candidate SNPs were observed in two candidate genes in chromosome 3 encoding a hydrolase (LOC_Os03g03200) or the gibberellin receptor GID1L2 (LOC_Os03g14730) and one in chromosome 5, LOC_Os05g08110 encoding a chloroplast precursor with orthologs in other plants encoding an isoamylase. The research reported here reveals genetic factors important to the control of the chalky phenotype in the IR64 background, knowledge that will help the further genetic improvement of rice.","abstract_html":"Abnormal endosperm development of rice (Oryza sativa L.) often produces a chalky phenotype, which strongly affects appearance, quality and grain weight. Although many enzymes and related regulators associated with endosperm chalk have been identified, many other related factors remain largely unknown. Here we describe a genetic screen for mutants with increased chalkiness from a mutagenized population of the rice mega-variety, IR64. From an initial population of 9853 M2 families, 41 were identified with heritable chalky phenotypes, which were also often associated with reductions in grain size. The M3848 mutant was unique in displaying a strong chalky phenotype but no change in seed size and was characterized in greater detail. The M3848 mutant has an opaque endosperm and abnormal starch granules and is inherited as a single locus recessive. Representative of the opaque/floury phenotype, grains of M3848 showed a higher grain percent chalkiness in comparison with that of IR64 Wild Type (IR64_WT). The contents of amylose in M3848 significantly decreased, while short chain amylopectins significantly increased and its physicochemical properties were also altered. DNA sequencing was used to identify single nucleotide polymorphisms (SNPs) highly enriched among plants displaying the M3848 mutant phenotype compared to siblings with normal phenotypes. Although these analyses did not clearly discover the causal mutation for the M3848 mutation, candidate SNPs were observed in two candidate genes in chromosome 3 encoding a hydrolase (LOC_Os03g03200) or the gibberellin receptor GID1L2 (LOC_Os03g14730) and one in chromosome 5, LOC_Os05g08110 encoding a chloroplast precursor with orthologs in other plants encoding an isoamylase. The research reported here reveals genetic factors important to the control of the chalky phenotype in the IR64 background, knowledge that will help the further genetic improvement of rice.","abstract_has_math":false,"creators":["Quiatchon-Baeza, Lenie Angeles"],"institution":"University of Illinois at Urbana-Champaign","degree_name":"Ph.D.","degree_level":"Dissertation","degree_discipline":"Crop Sciences","degree_department":null,"school":null,"contributors":["Moose, Stephen P.","Sreenivasulu, Nese","Juvik, John A.","Sacks, Erik"],"advisors":[],"committee_chairs":[],"committee_members":[],"year":2019,"date_issued":"2019-08-23T20:48:19Z","date_published":"2019-08-23T20:48:19Z","updated_at":"2026-07-22T22:24:44Z","subjects":["chalk MutMap mutants EMS IR64 rice grain quality"],"languages":["en"],"rights":["Copyright 2019 Lenie Quiatchon-Baeza"],"rights_urls":[],"identifier_entries":[]},"links":{"outbound_url":"http://hdl.handle.net/2142/105226","outbound_label":"Handle","outbound_source":"dc:identifier"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor","label":"Contributor","values":["Moose, Stephen P.","Sreenivasulu, Nese","Juvik, John A.","Sacks, Erik"]},{"key":"dc:creator","label":"Author","values":["Quiatchon-Baeza, Lenie Angeles"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date","label":"Dc Date","values":["2019-08-23T20:48:19Z","2021-08-24T09:15:31Z","2019-04-19","2019-05"]},{"key":"dc:type","label":"Dc Type","values":["text"]},{"key":"thesis:degree_discipline","label":"Discipline","values":["Crop Sciences"]},{"key":"thesis:degree_level","label":"Degree Level","values":["Dissertation"]},{"key":"thesis:degree_name","label":"Degree Name","values":["Ph.D."]},{"key":"thesis:institution_name","label":"Thesis Institution Name","values":["University of Illinois at Urbana-Champaign"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["chalk MutMap mutants EMS IR64 rice grain quality"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["en"]},{"key":"dc:rights","label":"Dc Rights","values":["Copyright 2019 Lenie Quiatchon-Baeza"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier","label":"Identifier","values":["http://hdl.handle.net/2142/105226"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description","label":"Description","values":["Abnormal endosperm development of rice (Oryza sativa L.) often produces a chalky phenotype, which strongly affects appearance, quality and grain weight. Although many enzymes and related regulators associated with endosperm chalk have been identified, many other related factors remain largely unknown. Here we describe a genetic screen for mutants with increased chalkiness from a mutagenized population of the rice mega-variety, IR64. From an initial population of 9853 M2 families, 41 were identified with heritable chalky phenotypes, which were also often associated with reductions in grain size. The M3848 mutant was unique in displaying a strong chalky phenotype but no change in seed size and was characterized in greater detail. The M3848 mutant has an opaque endosperm and abnormal starch granules and is inherited as a single locus recessive. Representative of the opaque/floury phenotype, grains of M3848 showed a higher grain percent chalkiness in comparison with that of IR64 Wild Type (IR64_WT). The contents of amylose in M3848 significantly decreased, while short chain amylopectins significantly increased and its physicochemical properties were also altered. DNA sequencing was used to identify single nucleotide polymorphisms (SNPs) highly enriched among plants displaying the M3848 mutant phenotype compared to siblings with normal phenotypes. Although these analyses did not clearly discover the causal mutation for the M3848 mutation, candidate SNPs were observed in two candidate genes in chromosome 3 encoding a hydrolase (LOC_Os03g03200) or the gibberellin receptor GID1L2 (LOC_Os03g14730) and one in chromosome 5, LOC_Os05g08110 encoding a chloroplast precursor with orthologs in other plants encoding an isoamylase. The research reported here reveals genetic factors important to the control of the chalky phenotype in the IR64 background, knowledge that will help the further genetic improvement of rice.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01","The student, Lenie Quiatchon-Baeza, accepted the attached license on 2019-04-18 at 15:25.","The student, Lenie Quiatchon-Baeza, submitted this Dissertation for approval on 2019-04-18 at 15:31.","This Dissertation was approved for publication on 2019-04-19 at 13:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13754 on 2019-08-22 at 16:23:15","Made available in DSpace on 2019-08-23T20:48:19Z (GMT). No. of bitstreams: 2 QUIATCHON-BAEZA-DISSERTATION-2019.pdf: 18303341 bytes, checksum: 0e284d3beecaec56ba5d2da6ed89fa26 (MD5) LICENSE.txt: 4218 bytes, checksum: 6e70758a809d53a452ab90e442dd847b (MD5) Previous issue date: 2019-04-19","Embargo set by: Seth Robbins for item 112348 Lift date: 2021-08-23T20:48:32Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 112348 on 2021-08-24T09:15:31Z."]},{"key":"dc:format","label":"Dc Format","values":["application/pdf"]},{"key":"dc:title","label":"Title","values":["Identification of causal mutations of grain chalkiness in rice EMS populations via mapping-by-sequencing"]}]}],"canonical_facts":{"dc:contributor":["Moose, Stephen P.","Sreenivasulu, Nese","Juvik, John A.","Sacks, Erik"],"dc:creator":["Quiatchon-Baeza, Lenie Angeles"],"dc:date":["2019-08-23T20:48:19Z","2021-08-24T09:15:31Z","2019-04-19","2019-05"],"dc:description":["Abnormal endosperm development of rice (Oryza sativa L.) often produces a chalky phenotype, which strongly affects appearance, quality and grain weight. Although many enzymes and related regulators associated with endosperm chalk have been identified, many other related factors remain largely unknown. Here we describe a genetic screen for mutants with increased chalkiness from a mutagenized population of the rice mega-variety, IR64. From an initial population of 9853 M2 families, 41 were identified with heritable chalky phenotypes, which were also often associated with reductions in grain size. The M3848 mutant was unique in displaying a strong chalky phenotype but no change in seed size and was characterized in greater detail. The M3848 mutant has an opaque endosperm and abnormal starch granules and is inherited as a single locus recessive. Representative of the opaque/floury phenotype, grains of M3848 showed a higher grain percent chalkiness in comparison with that of IR64 Wild Type (IR64_WT). The contents of amylose in M3848 significantly decreased, while short chain amylopectins significantly increased and its physicochemical properties were also altered. DNA sequencing was used to identify single nucleotide polymorphisms (SNPs) highly enriched among plants displaying the M3848 mutant phenotype compared to siblings with normal phenotypes. Although these analyses did not clearly discover the causal mutation for the M3848 mutation, candidate SNPs were observed in two candidate genes in chromosome 3 encoding a hydrolase (LOC_Os03g03200) or the gibberellin receptor GID1L2 (LOC_Os03g14730) and one in chromosome 5, LOC_Os05g08110 encoding a chloroplast precursor with orthologs in other plants encoding an isoamylase. The research reported here reveals genetic factors important to the control of the chalky phenotype in the IR64 background, knowledge that will help the further genetic improvement of rice.","Submission published under a 24 month embargo labeled 'Closed Access', the embargo will last until 2021-05-01","The student, Lenie Quiatchon-Baeza, accepted the attached license on 2019-04-18 at 15:25.","The student, Lenie Quiatchon-Baeza, submitted this Dissertation for approval on 2019-04-18 at 15:31.","This Dissertation was approved for publication on 2019-04-19 at 13:12.","DSpace SAF Submission Ingestion Package generated from Vireo submission #13754 on 2019-08-22 at 16:23:15","Made available in DSpace on 2019-08-23T20:48:19Z (GMT). No. of bitstreams: 2 QUIATCHON-BAEZA-DISSERTATION-2019.pdf: 18303341 bytes, checksum: 0e284d3beecaec56ba5d2da6ed89fa26 (MD5) LICENSE.txt: 4218 bytes, checksum: 6e70758a809d53a452ab90e442dd847b (MD5) Previous issue date: 2019-04-19","Embargo set by: Seth Robbins for item 112348 Lift date: 2021-08-23T20:48:32Z Reason: Author requested closed access (OA after 2yrs) in Vireo ETD system","Limited Restriction Lifted for Item 112348 on 2021-08-24T09:15:31Z."],"dc:format":["application/pdf"],"dc:identifier":["http://hdl.handle.net/2142/105226"],"dc:language":["en"],"dc:rights":["Copyright 2019 Lenie Quiatchon-Baeza"],"dc:subject":["chalk MutMap mutants EMS IR64 rice grain quality"],"dc:title":["Identification of causal mutations of grain chalkiness in rice EMS populations via mapping-by-sequencing"],"dc:type":["text"],"thesis:degree_discipline":["Crop Sciences"],"thesis:degree_level":["Dissertation"],"thesis:degree_name":["Ph.D."],"thesis:institution_name":["University of Illinois at Urbana-Champaign"]},"updated_at":"2026-07-22T22:24:44Z"}