Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

Zhi Hong Zhang; Xin Shun Qu; Shan Wan; Li Hua Chen; Ying Guo Zhu

doi:10.1093/aob/mci039

Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

Zhi Hong Zhang, Xin Shun Qu, Shan Wan, Li Hua Chen, Ying Guo Zhu

Plant Pathology and Environmental Microbiology

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

100 Scopus citations

Abstract

• Background and Aims: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype X environmental temperature interactions for seedling vigour QTL. • Methods: A set of 282 F₁₃ recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25°C, 20°C and 15°C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. • Key Results: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82 %) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20°C and 25°C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. • Conclusions: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.

Original language	English (US)
Pages (from-to)	423-429
Number of pages	7
Journal	Annals of botany
Volume	95
Issue number	3
DOIs	https://doi.org/10.1093/aob/mci039
State	Published - 2005

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Plant Science

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10.1093/aob/mci039

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@article{e3b2b0d7c3624239b5e93f53c1779c63,

title = "Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)",

abstract = "• Background and Aims: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype X environmental temperature interactions for seedling vigour QTL. • Methods: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25°C, 20°C and 15°C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. • Key Results: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82 %) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20°C and 25°C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. • Conclusions: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.",

author = "Zhang, {Zhi Hong} and Qu, {Xin Shun} and Shan Wan and Chen, {Li Hua} and Zhu, {Ying Guo}",

note = "Funding Information: We thank Dr B.Y. Fu and Dr Z.K. Li of the International Rice Research Institute (IRRI) for providing the {\textquoteleft}Lemont{\textquoteright}/ {\textquoteleft}Teqing{\textquoteright} RIL population and the marker data. We also thank Professor S.B. Yu of Huazhong Agricultural University for his help in the construction of the genetic map. We are grateful to the undergraduate students A.L. Niu, X.L. Lu, H.B. Cui and Q.Y. Bi of the College of Life Sciences for helping to collect the phenotypic data. This work was supported by the State {\textquoteleft}973{\textquoteright} Project (2001CB108806) of China.",

year = "2005",

doi = "10.1093/aob/mci039",

language = "English (US)",

volume = "95",

pages = "423--429",

journal = "Annals of botany",

issn = "0305-7364",

publisher = "Oxford University Press",

number = "3",

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TY - JOUR

T1 - Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

AU - Zhang, Zhi Hong

AU - Qu, Xin Shun

AU - Wan, Shan

AU - Chen, Li Hua

AU - Zhu, Ying Guo

N1 - Funding Information: We thank Dr B.Y. Fu and Dr Z.K. Li of the International Rice Research Institute (IRRI) for providing the ‘Lemont’/ ‘Teqing’ RIL population and the marker data. We also thank Professor S.B. Yu of Huazhong Agricultural University for his help in the construction of the genetic map. We are grateful to the undergraduate students A.L. Niu, X.L. Lu, H.B. Cui and Q.Y. Bi of the College of Life Sciences for helping to collect the phenotypic data. This work was supported by the State ‘973’ Project (2001CB108806) of China.

PY - 2005

Y1 - 2005

N2 - • Background and Aims: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype X environmental temperature interactions for seedling vigour QTL. • Methods: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25°C, 20°C and 15°C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. • Key Results: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82 %) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20°C and 25°C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. • Conclusions: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.

AB - • Background and Aims: Seedling vigour is one of the major determinants for stable stand establishment in rice (Oryza sativa), especially in a direct seeding cropping system. The objectives of this study were to identify superior alleles with consistent effects on seedling vigour across different temperature conditions and to investigate genotype X environmental temperature interactions for seedling vigour QTL. • Methods: A set of 282 F13 recombinant inbred lines (RILs) derived from a rice cross were assessed for four seedling vigour traits at three temperatures (25°C, 20°C and 15°C). Using a linkage map with 198 marker loci, the main-effect QTL for the traits were mapped by composite interval mapping. • Key Results: A total of 34 QTL for the four seedling vigour traits were identified. Of these QTL, the majority (82 %) were clustered within five genomic regions, designated as QTL qSV-3-1, qSV-3-2, qSV-5, qSV-8-1 and qSV-8-2. All of these five QTL had small individual effects on the traits, explaining 3.1-15.8 % of the phenotypic variation with a mean of 7.3 %. QTL qSV-3-1, qSV-3-2 and qSV-8-1 showed almost consistent effects on the traits across all three temperatures while qSV-5 and qSV-8-2 had effects mainly at the 'normal' temperatures of 20°C and 25°C. Among the five QTL identified, all and four showed additive effects on shoot length and germination rate, respectively. The contributions of these five QTL to shoot length and germination rate were also much larger than those to the other two traits. • Conclusions: A few of genomic regions (or QTL) were identified as showing effects on seedling vigour. For these QTL, significant genotype x environmental temperature interactions were found and these interactions appeared to be QTL-specific. Among the four seedling vigour traits measured, shoot length and germination rate could be used as relatively good indicators to evaluate the level of seedling vigour in rice.

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DO - 10.1093/aob/mci039

M3 - Article

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AN - SCOPUS:14944350442

SN - 0305-7364

VL - 95

SP - 423

EP - 429

JO - Annals of botany

JF - Annals of botany

IS - 3

ER -

Comparison of QTL controlling seedling vigour under different temperature conditions using recombinant inbred lines in rice (Oryza sativa)

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