Identification of causal mutations of grain chalkiness in rice EMS populations via mapping-by-sequencing

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.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Crop Sciences

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2019

Author dc:creator

• Quiatchon-Baeza, Lenie Angeles

Contributors dc:contributor

• Moose, Stephen P.
• Sreenivasulu, Nese
• Juvik, John A.
• Sacks, Erik

• chalk MutMap mutants EMS IR64 rice grain quality

Statement dc:rights

• Copyright 2019 Lenie Quiatchon-Baeza

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/105226

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/105226