QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

Ying Zhang; Catherine L Thomas; Jinxia Xiang; Yan Long; Xiaohua Wang; Jun Zou; Ziliang Luo; Guangda Ding; Hongmei Cai; Neil S Graham; John P Hammond; Graham J King; Philip J White; Fangsen Xu; Martin R Broadley; Lei Shi; Jinling Meng

doi:10.1038/srep33113

QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

Ying Zhang, Catherine L Thomas, Jinxia Xiang, Yan Long, Xiaohua Wang, Jun Zou, Ziliang Luo, Guangda Ding, Hongmei Cai, Neil S Graham, John P Hammond, Graham J King, Philip J White, Fangsen Xu, Martin R Broadley, Lei Shi (Lead / Corresponding author), Jinling Meng

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Abstract

A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.

Original language	English
Article number	33113
Pages (from-to)	1-12
Number of pages	12
Journal	Scientific Reports
Volume	6
DOIs	https://doi.org/10.1038/srep33113
Publication status	Published - 14 Sept 2016

Keywords

Brassica napus/genetics
Phosphorus/pharmacology
Plant Roots/genetics
Plant Shoots/genetics
Polymorphism, Single Nucleotide
Quantitative Trait, Heritable

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10.1038/srep33113Licence: CC BY

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Final published version, 1.41 MBLicence: CC BY

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Zhang, Y., Thomas, C. L., Xiang, J., Long, Y., Wang, X., Zou, J., Luo, Z., Ding, G., Cai, H., Graham, N. S., Hammond, J. P., King, G. J., White, P. J., Xu, F., Broadley, M. R., Shi, L., & Meng, J. (2016). QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems. Scientific Reports, 6, 1-12. Article 33113. https://doi.org/10.1038/srep33113

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title = "QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems",

abstract = "A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.",

keywords = "Brassica napus/genetics, Phosphorus/pharmacology, Plant Roots/genetics, Plant Shoots/genetics, Polymorphism, Single Nucleotide, Quantitative Trait, Heritable",

author = "Ying Zhang and Thomas, {Catherine L} and Jinxia Xiang and Yan Long and Xiaohua Wang and Jun Zou and Ziliang Luo and Guangda Ding and Hongmei Cai and Graham, {Neil S} and Hammond, {John P} and King, {Graham J} and White, {Philip J} and Fangsen Xu and Broadley, {Martin R} and Lei Shi and Jinling Meng",

note = "The authors acknowledge the financial support from the UK BBSRC (CIRC Project BB/J019631/1; International Partnering Award BB/J020443/1), National Nature Science Foundation of China (Grant No. 31471933), New Century Excellent Talents in University of Ministry of Education of China (Grant No. NCET-13-0809), Natural and Fundamental Research Funds for the Central Universities of China (Grant No. 2014PY020; 2662015PY105), Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government through WorkPackage 3.3 (2011–2016).",

year = "2016",

month = sep,

day = "14",

doi = "10.1038/srep33113",

language = "English",

volume = "6",

pages = "1--12",

journal = "Scientific Reports",

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T1 - QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

AU - Zhang, Ying

AU - Thomas, Catherine L

AU - Xiang, Jinxia

AU - Long, Yan

AU - Wang, Xiaohua

AU - Zou, Jun

AU - Luo, Ziliang

AU - Ding, Guangda

AU - Cai, Hongmei

AU - Graham, Neil S

AU - Hammond, John P

AU - King, Graham J

AU - White, Philip J

AU - Xu, Fangsen

AU - Broadley, Martin R

AU - Shi, Lei

AU - Meng, Jinling

N1 - The authors acknowledge the financial support from the UK BBSRC (CIRC Project BB/J019631/1; International Partnering Award BB/J020443/1), National Nature Science Foundation of China (Grant No. 31471933), New Century Excellent Talents in University of Ministry of Education of China (Grant No. NCET-13-0809), Natural and Fundamental Research Funds for the Central Universities of China (Grant No. 2014PY020; 2662015PY105), Rural and Environment Science and Analytical Services Division (RESAS) of the Scottish Government through WorkPackage 3.3 (2011–2016).

PY - 2016/9/14

Y1 - 2016/9/14

N2 - A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.

AB - A high-density SNP-based genetic linkage map was constructed and integrated with a previous map in the Tapidor x Ningyou7 (TNDH) Brassica napus population, giving a new map with a total of 2041 molecular markers and an average marker density which increased from 0.39 to 0.97 (0.82 SNP bin) per cM. Root and shoot traits were screened under low and 'normal' phosphate (Pi) supply using a 'pouch and wick' system, and had been screened previously in an agar based system. The P-efficient parent Ningyou7 had a shorter primary root length (PRL), greater lateral root density (LRD) and a greater shoot biomass than the P-inefficient parent Tapidor under both treatments and growth systems. Quantitative trait loci (QTL) analysis identified a total of 131 QTL, and QTL meta-analysis found four integrated QTL across the growth systems. Integration reduced the confidence interval by ~41%. QTL for root and shoot biomass were co-located on chromosome A3 and for lateral root emergence were co-located on chromosomes A4/C4 and C8/C9. There was a major QTL for LRD on chromosome C9 explaining ~18% of the phenotypic variation. QTL underlying an increased LRD may be a useful breeding target for P uptake efficiency in Brassica.

KW - Brassica napus/genetics

KW - Phosphorus/pharmacology

KW - Plant Roots/genetics

KW - Plant Shoots/genetics

KW - Polymorphism, Single Nucleotide

KW - Quantitative Trait, Heritable

U2 - 10.1038/srep33113

DO - 10.1038/srep33113

M3 - Article

C2 - 27624881

SN - 2045-2322

VL - 6

SP - 1

EP - 12

JO - Scientific Reports

JF - Scientific Reports

M1 - 33113

ER -

QTL meta-analysis of root traits in Brassica napus under contrasting phosphorus supply in two growth systems

Abstract

Keywords

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