Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length

Dharminder Bhatia, Rod A Wing, Yeisoo Yu, Kapeel Chougule, David A Kudrna, Seunghee Lee, Allah Rang, Kuldeep Singh

Research output: Contribution to journalArticle

7 Citations (Scopus)

Abstract

Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.

Original languageEnglish (US)
Article number41
JournalEuphytica
Volume214
Issue number2
DOIs
StatePublished - Feb 1 2018

Fingerprint

inbred lines
genotyping
quantitative trait loci
Weights and Measures
rice
Single Nucleotide Polymorphism
Alleles
additive effect
Pedigree
Oryza
alleles
wild rice
wild relatives
consumer preferences
pedigree
yield components
genetic background
data analysis

Keywords

  • Backcross inbred lines (BILs)
  • Genotyping by sequencing (GBS)
  • Grain length
  • Grain weight
  • O. glumaepatula
  • O. rufipogon
  • Quantitative trait loci (QTL)

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Genetics
  • Plant Science
  • Horticulture

Cite this

Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. / Bhatia, Dharminder; Wing, Rod A; Yu, Yeisoo; Chougule, Kapeel; Kudrna, David A; Lee, Seunghee; Rang, Allah; Singh, Kuldeep.

In: Euphytica, Vol. 214, No. 2, 41, 01.02.2018.

Research output: Contribution to journalArticle

Bhatia, Dharminder ; Wing, Rod A ; Yu, Yeisoo ; Chougule, Kapeel ; Kudrna, David A ; Lee, Seunghee ; Rang, Allah ; Singh, Kuldeep. / Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length. In: Euphytica. 2018 ; Vol. 214, No. 2.
@article{6c811213bffe4182ad91344d217d7644,
title = "Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length",
abstract = "Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.",
keywords = "Backcross inbred lines (BILs), Genotyping by sequencing (GBS), Grain length, Grain weight, O. glumaepatula, O. rufipogon, Quantitative trait loci (QTL)",
author = "Dharminder Bhatia and Wing, {Rod A} and Yeisoo Yu and Kapeel Chougule and Kudrna, {David A} and Seunghee Lee and Allah Rang and Kuldeep Singh",
year = "2018",
month = "2",
day = "1",
doi = "10.1007/s10681-018-2119-1",
language = "English (US)",
volume = "214",
journal = "Euphytica",
issn = "0014-2336",
publisher = "Springer Netherlands",
number = "2",

}

TY - JOUR

T1 - Genotyping by sequencing of rice interspecific backcross inbred lines identifies QTLs for grain weight and grain length

AU - Bhatia, Dharminder

AU - Wing, Rod A

AU - Yu, Yeisoo

AU - Chougule, Kapeel

AU - Kudrna, David A

AU - Lee, Seunghee

AU - Rang, Allah

AU - Singh, Kuldeep

PY - 2018/2/1

Y1 - 2018/2/1

N2 - Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.

AB - Grain weight and grain length are the most stable components of rice yield and important indicators of consumer preference. Considering the potentials of wild rice and to enhance the rice yields to meet the increasing demands, 185 Backcross Inbred Lines (BILs) in the background of O. sativa ssp. indica cv. PR114, including 63 rufi-BILs derived from O. rufipogon IRGC104433 and 122 glumae-BILs from O. glumaepatula IRGC104387 were evaluated for mapping QTLs for yield and yield component traits using Genotyping by Sequencing (GBS). Phenotypic evaluation of BILs in three seasons spanning two locations revealed significant differences compared with recurrent parent. BILs which did not show significant differences for any trait under investigation, or similar based on pedigree, were excluded from GBS. Some glumae-BILs had to be excluded from mapping QTLs due to less sequence information. A custom designed approach for GBS data analysis identified 3322 informative SNPs in 55 rufi-BILs and 3437 informative SNPs in 79 glumae-BILs. QTL mapping identified one QTL for thousand grain weight (qtgw5.1), two for grain width (qgw5.1, qgw5.2) and one for grain length (qgl7.1) in rufi-BILs. In the glumae-BILs, three QTL for thousand grain weight (qtgw2.1, qtgw3.1, qtgw6.1) and two for grain length (qgl3.1, qgl7.1) were identified. Most of the grain weight and width QTL showed positive additive effect contributed by wild species allele, whereas the grain length QTL showed positive additive effect contributed by recurrent parent allele. Based on their physical position, none of the QTLs were found similar to previously cloned QTLs. QTLs for grain traits identified from low yielding wild relatives of rice reveals their significance in improving further the rice yields and widen the genetic base of cultivated rice.

KW - Backcross inbred lines (BILs)

KW - Genotyping by sequencing (GBS)

KW - Grain length

KW - Grain weight

KW - O. glumaepatula

KW - O. rufipogon

KW - Quantitative trait loci (QTL)

UR - http://www.scopus.com/inward/record.url?scp=85041299898&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=85041299898&partnerID=8YFLogxK

U2 - 10.1007/s10681-018-2119-1

DO - 10.1007/s10681-018-2119-1

M3 - Article

AN - SCOPUS:85041299898

VL - 214

JO - Euphytica

JF - Euphytica

SN - 0014-2336

IS - 2

M1 - 41

ER -