Genetic dissection of grain nutritional traits and leaf blight resistance in rice

Gwen Iris Descalsota-Empleo, Noraziyah Abd Aziz Shamsudin, Ian Paul Navea, Chongtae Chung, Maria Stefanie Dwiyanti, Reuben Jacob Dicen Labios, Asmuni Mohd Ikmal, Venice Margarette Juanillas, Mary Ann Inabangan-Asilo, Amery Amparado, Russell Reinke, Casiana M. Vera Cruz, Joong Hyoun Chin, B. P. Mallikarjuna Swamy

Research output: Contribution to journalArticle

Abstract

Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

Original languageEnglish
Article number30
JournalGenes
Volume10
Issue number1
DOIs
Publication statusPublished - 1 Jan 2019

Fingerprint

Dissection
Linkage Disequilibrium
Breeding
Disease Resistance
Anthocyanins
Quantitative Trait Loci
Genome-Wide Association Study
Single Nucleotide Polymorphism
Zinc
Genes
Normal Distribution
Oryza
Principal Component Analysis
Genetic Recombination
Minerals
Antioxidants
Alleles
Genotype

Keywords

  • Anthocyanin
  • Association mapping
  • Bacterial leaf blight
  • Colored rice
  • Fe
  • Genome-wide
  • Nutritional content
  • QTLs
  • Zn

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Descalsota-Empleo, G. I., Abd Aziz Shamsudin, N., Navea, I. P., Chung, C., Dwiyanti, M. S., Labios, R. J. D., ... Mallikarjuna Swamy, B. P. (2019). Genetic dissection of grain nutritional traits and leaf blight resistance in rice. Genes, 10(1), [30]. https://doi.org/10.3390/genes10010030

Genetic dissection of grain nutritional traits and leaf blight resistance in rice. / Descalsota-Empleo, Gwen Iris; Abd Aziz Shamsudin, Noraziyah; Navea, Ian Paul; Chung, Chongtae; Dwiyanti, Maria Stefanie; Labios, Reuben Jacob Dicen; Ikmal, Asmuni Mohd; Juanillas, Venice Margarette; Inabangan-Asilo, Mary Ann; Amparado, Amery; Reinke, Russell; Vera Cruz, Casiana M.; Chin, Joong Hyoun; Mallikarjuna Swamy, B. P.

In: Genes, Vol. 10, No. 1, 30, 01.01.2019.

Research output: Contribution to journalArticle

Descalsota-Empleo, GI, Abd Aziz Shamsudin, N, Navea, IP, Chung, C, Dwiyanti, MS, Labios, RJD, Ikmal, AM, Juanillas, VM, Inabangan-Asilo, MA, Amparado, A, Reinke, R, Vera Cruz, CM, Chin, JH & Mallikarjuna Swamy, BP 2019, 'Genetic dissection of grain nutritional traits and leaf blight resistance in rice', Genes, vol. 10, no. 1, 30. https://doi.org/10.3390/genes10010030
Descalsota-Empleo GI, Abd Aziz Shamsudin N, Navea IP, Chung C, Dwiyanti MS, Labios RJD et al. Genetic dissection of grain nutritional traits and leaf blight resistance in rice. Genes. 2019 Jan 1;10(1). 30. https://doi.org/10.3390/genes10010030
Descalsota-Empleo, Gwen Iris ; Abd Aziz Shamsudin, Noraziyah ; Navea, Ian Paul ; Chung, Chongtae ; Dwiyanti, Maria Stefanie ; Labios, Reuben Jacob Dicen ; Ikmal, Asmuni Mohd ; Juanillas, Venice Margarette ; Inabangan-Asilo, Mary Ann ; Amparado, Amery ; Reinke, Russell ; Vera Cruz, Casiana M. ; Chin, Joong Hyoun ; Mallikarjuna Swamy, B. P. / Genetic dissection of grain nutritional traits and leaf blight resistance in rice. In: Genes. 2019 ; Vol. 10, No. 1.
@article{50584283b0f44260b7deb3bd4ccb6204,
title = "Genetic dissection of grain nutritional traits and leaf blight resistance in rice",
abstract = "Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3{\%} of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36{\%} of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9{\%} to 18{\%}. Interestingly, 30 (53{\%}) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.",
keywords = "Anthocyanin, Association mapping, Bacterial leaf blight, Colored rice, Fe, Genome-wide, Nutritional content, QTLs, Zn",
author = "Descalsota-Empleo, {Gwen Iris} and {Abd Aziz Shamsudin}, Noraziyah and Navea, {Ian Paul} and Chongtae Chung and Dwiyanti, {Maria Stefanie} and Labios, {Reuben Jacob Dicen} and Ikmal, {Asmuni Mohd} and Juanillas, {Venice Margarette} and Inabangan-Asilo, {Mary Ann} and Amery Amparado and Russell Reinke and {Vera Cruz}, {Casiana M.} and Chin, {Joong Hyoun} and {Mallikarjuna Swamy}, {B. P.}",
year = "2019",
month = "1",
day = "1",
doi = "10.3390/genes10010030",
language = "English",
volume = "10",
journal = "Genes",
issn = "2073-4425",
publisher = "Multidisciplinary Digital Publishing Institute (MDPI)",
number = "1",

}

TY - JOUR

T1 - Genetic dissection of grain nutritional traits and leaf blight resistance in rice

AU - Descalsota-Empleo, Gwen Iris

AU - Abd Aziz Shamsudin, Noraziyah

AU - Navea, Ian Paul

AU - Chung, Chongtae

AU - Dwiyanti, Maria Stefanie

AU - Labios, Reuben Jacob Dicen

AU - Ikmal, Asmuni Mohd

AU - Juanillas, Venice Margarette

AU - Inabangan-Asilo, Mary Ann

AU - Amparado, Amery

AU - Reinke, Russell

AU - Vera Cruz, Casiana M.

AU - Chin, Joong Hyoun

AU - Mallikarjuna Swamy, B. P.

PY - 2019/1/1

Y1 - 2019/1/1

N2 - Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

AB - Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.

KW - Anthocyanin

KW - Association mapping

KW - Bacterial leaf blight

KW - Colored rice

KW - Fe

KW - Genome-wide

KW - Nutritional content

KW - QTLs

KW - Zn

UR - http://www.scopus.com/inward/record.url?scp=85060578864&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85060578864&partnerID=8YFLogxK

U2 - 10.3390/genes10010030

DO - 10.3390/genes10010030

M3 - Article

VL - 10

JO - Genes

JF - Genes

SN - 2073-4425

IS - 1

M1 - 30

ER -