Genetic loci regulating arsenic content in rice grains when grown flooded or under alternative wetting and drying irrigation

Gareth Norton (Corresponding Author), Anthony J Travis, Partha Talukdar, Mahmud Hossain Sumon, Md Rafiqul, Adam H Price (Corresponding Author)

Research output: Contribution to journalArticle

Abstract

Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic.

Results
AWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic.

All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL.

Conclusions
This study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied.
Original languageEnglish
Article number54
JournalRice
Volume12
DOIs
Publication statusPublished - 22 Jul 2019

Fingerprint

arsenic
wetting
rice
drying
irrigation
loci
cultivar
quantitative trait loci
high-yielding varieties
chromosome
cultivars
chromosome mapping
chromosomes
genome
water management
haplotypes
shoot
crop
shoots
gene

Keywords

  • rice
  • arsenic
  • genome wide association genetics
  • alternate wetting and drying
  • Arsenic
  • Alternate wetting and drying
  • Genome wide association genetics
  • Rice
  • WATER-USE
  • TRANSPORTER
  • YIELD
  • IDENTIFICATION
  • QUANTITATIVE TRAIT LOCI
  • CULTIVARS
  • METABOLISM
  • NITROGEN
  • ACCUMULATION
  • ASSOCIATION

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

Cite this

@article{cf776906e5ad4b7ca4c7ec8e3e013446,
title = "Genetic loci regulating arsenic content in rice grains when grown flooded or under alternative wetting and drying irrigation",
abstract = "Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic.ResultsAWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1{\%} in year 1 and 2 respectively and shoot arsenic by 27.0{\%} compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic.All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL.ConclusionsThis study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10{\%} in all high yielding cultivars studied.",
keywords = "rice, arsenic, genome wide association genetics, alternate wetting and drying, Arsenic, Alternate wetting and drying, Genome wide association genetics, Rice, WATER-USE, TRANSPORTER, YIELD, IDENTIFICATION, QUANTITATIVE TRAIT LOCI, CULTIVARS, METABOLISM, NITROGEN, ACCUMULATION, ASSOCIATION",
author = "Gareth Norton and Travis, {Anthony J} and Partha Talukdar and Sumon, {Mahmud Hossain} and Md Rafiqul and Price, {Adam H}",
note = "The 2 M SNP genotype data of the BAAP is available as a project called “BAAP” at the SNP-Seek database (http://snp-seek.irri.org/). The phenotype data used for the GWAS is presented in Additional file 1: Table S1. The bulk of this work was supported by the Biotechnology and Biological Sciences Research Council, mostly from project BB/J003336/1, while a small part of the work by AJT was also supported by project BB/N013492/1 (NEWS-India-UK). Plant material was imported into the UK under import licence IMP/SOIL/19/2014.",
year = "2019",
month = "7",
day = "22",
doi = "10.1186/s12284-019-0307-9",
language = "English",
volume = "12",
journal = "Rice",
issn = "1939-8433",
publisher = "Springer Publishing Company",

}

TY - JOUR

T1 - Genetic loci regulating arsenic content in rice grains when grown flooded or under alternative wetting and drying irrigation

AU - Norton, Gareth

AU - Travis, Anthony J

AU - Talukdar, Partha

AU - Sumon, Mahmud Hossain

AU - Rafiqul, Md

AU - Price, Adam H

N1 - The 2 M SNP genotype data of the BAAP is available as a project called “BAAP” at the SNP-Seek database (http://snp-seek.irri.org/). The phenotype data used for the GWAS is presented in Additional file 1: Table S1. The bulk of this work was supported by the Biotechnology and Biological Sciences Research Council, mostly from project BB/J003336/1, while a small part of the work by AJT was also supported by project BB/N013492/1 (NEWS-India-UK). Plant material was imported into the UK under import licence IMP/SOIL/19/2014.

PY - 2019/7/22

Y1 - 2019/7/22

N2 - Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic.ResultsAWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic.All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL.ConclusionsThis study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied.

AB - Rice is a global staple crop, being the main calorific component of many people living subsistence livelihoods. Rice can accumulate toxic elements such as arsenic, with the crop water management strongly affecting uptake. This study utilises the Bengal and Assam Aus Panel to conduct genome wide association (GWA) mapping for arsenic in shoots and grains of rice grown over 2 years under continually flooded (CF) and alternate wetting and drying (AWD). The aim was to assess genotype by water management interaction, identify quantitative trait loci (QTL) for arsenic accumulation, and propose candidate genes for lowering grain arsenic.ResultsAWD significantly reduced grain arsenic across all cultivars on average by 15.7 and 15.1% in year 1 and 2 respectively and shoot arsenic by 27.0% compared to the plants grown under CF. There was a weak cultivar by treatment interaction for grain for arsenic.All traits were strongly influenced by cultivar. GWA mapping identified a large number of 74 individual QTLs for arsenic, with six QTLs showing stability across years and/or water treatments. Three of the loci (one on chromosome 3, one on chromosome 4, and one on chromosome 5) were investigated in detail using an approach of clustering cultivars that had similar haplotypes for the QTL regions and then looking at the phenotypic values across the clusters. Two of the identified QTLs co-localised with known genes involved in arsenic accumulation, including Lsi2 which has not previously been reported to underlie a grain arsenic QTL.ConclusionsThis study has identified a number of novel QTLs for arsenic accumulation, as well as cultivars that consistently accumulate less arsenic over multiple field traits. The use of a haplotype clustering approach after GWA mapping has allowed for the effect, in terms of arsenic accumulation, to be determined for cultivars that share similar genomic sequence. Allocating nine high yielding Bangladeshi cultivars to these clusters has identified the potential of utilising these QTLs in breeding programmes; for example, incorporation of the QTL on chromosome 5 should decrease grain arsenic in elite high yielding Bangladeshi cultivars by 10% in all high yielding cultivars studied.

KW - rice

KW - arsenic

KW - genome wide association genetics

KW - alternate wetting and drying

KW - Arsenic

KW - Alternate wetting and drying

KW - Genome wide association genetics

KW - Rice

KW - WATER-USE

KW - TRANSPORTER

KW - YIELD

KW - IDENTIFICATION

KW - QUANTITATIVE TRAIT LOCI

KW - CULTIVARS

KW - METABOLISM

KW - NITROGEN

KW - ACCUMULATION

KW - ASSOCIATION

UR - http://www.scopus.com/inward/record.url?scp=85069454267&partnerID=8YFLogxK

UR - http://www.mendeley.com/research/genetic-loci-regulating-arsenic-content-rice-grains-grown-flooded-under-alternative-wetting-drying-i

U2 - 10.1186/s12284-019-0307-9

DO - 10.1186/s12284-019-0307-9

M3 - Article

VL - 12

JO - Rice

JF - Rice

SN - 1939-8433

M1 - 54

ER -