Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

Harsh Raman; Rosy Raman; Ramethaa Pirathiban; Brett McVittie; Niharika Sharma; Shengyi Liu; Yu Qiu; Anyu Zhu; Andrzej Kilian; Brian Cullis; Graham D. Farquhar; Hilary Stuart-Williams; Rosemary White; David Tabah; Andrew Easton; Yuanyuan Zhang

doi:10.1111/pce.14337

Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

Harsh Raman^*, Rosy Raman, Ramethaa Pirathiban, Brett McVittie, Niharika Sharma, Shengyi Liu, Yu Qiu, Anyu Zhu, Andrzej Kilian, Brian Cullis, Graham D. Farquhar, Hilary Stuart-Williams, Rosemary White, David Tabah, Andrew Easton, Yuanyuan Zhang^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

10 Citations (Scopus)

Abstract

Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ¹³C) in an F₂ population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ¹³C QTL. QTL contributing to main and QTL × environment interaction effects for Δ¹³C and yield were identified. One multiple-trait QTL for Δ¹³C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ¹³C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.

Original language	English
Pages (from-to)	2019-2036
Number of pages	18
Journal	Plant, Cell and Environment
Volume	45
Issue number	7
DOIs	https://doi.org/10.1111/pce.14337
Publication status	Published - Jul 2022

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Raman, H., Raman, R., Pirathiban, R., McVittie, B., Sharma, N., Liu, S., Qiu, Y., Zhu, A., Kilian, A., Cullis, B., Farquhar, G. D., Stuart-Williams, H., White, R., Tabah, D., Easton, A., & Zhang, Y. (2022). Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola. Plant, Cell and Environment, 45(7), 2019-2036. https://doi.org/10.1111/pce.14337

@article{12c9d5f90f3b429e8c611d4563988fd1,

title = "Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola",

abstract = "Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13C and yield were identified. One multiple-trait QTL for Δ13C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.",

keywords = "carbon isotope discrimination, drought avoidance, gene expression, genetic analysis, physiology, water use",

author = "Harsh Raman and Rosy Raman and Ramethaa Pirathiban and Brett McVittie and Niharika Sharma and Shengyi Liu and Yu Qiu and Anyu Zhu and Andrzej Kilian and Brian Cullis and Farquhar, {Graham D.} and Hilary Stuart-Williams and Rosemary White and David Tabah and Andrew Easton and Yuanyuan Zhang",

note = "Publisher Copyright: {\textcopyright} 2022 State of New South Wales. Plant, Cell & Environment published by John Wiley & Sons Ltd.",

year = "2022",

month = jul,

doi = "10.1111/pce.14337",

language = "English",

volume = "45",

pages = "2019--2036",

journal = "Plant, Cell and Environment",

issn = "0140-7791",

publisher = "Wiley-Blackwell Publishing Ltd",

number = "7",

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Raman, H, Raman, R, Pirathiban, R, McVittie, B, Sharma, N, Liu, S, Qiu, Y, Zhu, A, Kilian, A, Cullis, B, Farquhar, GD, Stuart-Williams, H, White, R, Tabah, D, Easton, A & Zhang, Y 2022, 'Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola', Plant, Cell and Environment, vol. 45, no. 7, pp. 2019-2036. https://doi.org/10.1111/pce.14337

TY - JOUR

T1 - Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

AU - Raman, Harsh

AU - Raman, Rosy

AU - Pirathiban, Ramethaa

AU - McVittie, Brett

AU - Sharma, Niharika

AU - Liu, Shengyi

AU - Qiu, Yu

AU - Zhu, Anyu

AU - Kilian, Andrzej

AU - Cullis, Brian

AU - Farquhar, Graham D.

AU - Stuart-Williams, Hilary

AU - White, Rosemary

AU - Tabah, David

AU - Easton, Andrew

AU - Zhang, Yuanyuan

PY - 2022/7

Y1 - 2022/7

N2 - Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13C and yield were identified. One multiple-trait QTL for Δ13C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.

AB - Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid population was analysed to identify quantitative trait loci (QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (Δ13C) in an F2 population. RNA sequencing was performed to determine the expression of candidate genes underlying Δ13C QTL. QTL contributing to main and QTL × environment interaction effects for Δ13C and yield were identified. One multiple-trait QTL for Δ13C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange (HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying Δ13C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.

KW - carbon isotope discrimination

KW - drought avoidance

KW - gene expression

KW - genetic analysis

KW - physiology

KW - water use

UR - http://www.scopus.com/inward/record.url?scp=85129372261&partnerID=8YFLogxK

U2 - 10.1111/pce.14337

DO - 10.1111/pce.14337

M3 - Article

SN - 0140-7791

VL - 45

SP - 2019

EP - 2036

JO - Plant, Cell and Environment

JF - Plant, Cell and Environment

IS - 7

ER -

Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

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