Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

R Wickneswari V Ratnam, M. A R Bhuiyan, Sabu K. Kalluvettankuzhy, Li Sze Lim, Michael J. Thomson, Md Kairudin Narimah, Md Zain Abdullah

Research output: Contribution to journalArticle

20 Citations (Scopus)

Abstract

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC 2F 2 population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16. 2 cM, spanning 1,553. 4 cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3. 0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC 2F 2 families, 26 advanced backcross breeding lines (BC 2F 5) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC 2F 3 and BC 2F 4 generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC 2F 5 generation whereas 29 QTLs were detected in BC 2F 2 generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R 2 values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC 2F 5 population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.

Original languageEnglish
Pages (from-to)929-939
Number of pages11
JournalPlant Molecular Biology Reporter
Volume30
Issue number4
DOIs
Publication statusPublished - Aug 2012

Fingerprint

Oryza rufipogon
Quantitative Trait Loci
backcrossing
breeding lines
agronomic traits
Breeding
quantitative trait loci
Oryza sativa
cultivars
Population
Oryza
rice
Genetic Linkage
plant morphology
Malaysia
yield components
Microsatellite Repeats
chromosome mapping
field experimentation

Keywords

  • Backcross breeding
  • Composite interval mapping
  • Oryza rufipogon
  • Oryza sativa
  • QTL identification
  • QTL validation
  • Trait-based marker analysis

ASJC Scopus subject areas

  • Plant Science
  • Molecular Biology

Cite this

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219. / V Ratnam, R Wickneswari; Bhuiyan, M. A R; Kalluvettankuzhy, Sabu K.; Lim, Li Sze; Thomson, Michael J.; Narimah, Md Kairudin; Abdullah, Md Zain.

In: Plant Molecular Biology Reporter, Vol. 30, No. 4, 08.2012, p. 929-939.

Research output: Contribution to journalArticle

V Ratnam, R Wickneswari ; Bhuiyan, M. A R ; Kalluvettankuzhy, Sabu K. ; Lim, Li Sze ; Thomson, Michael J. ; Narimah, Md Kairudin ; Abdullah, Md Zain. / Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219. In: Plant Molecular Biology Reporter. 2012 ; Vol. 30, No. 4. pp. 929-939.
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abstract = "A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC 2F 2 population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16. 2 cM, spanning 1,553. 4 cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3. 0). The O. rufipogon allele was favourable for 59{\%} of QTLs detected through CIM. Of 261 BC 2F 2 families, 26 advanced backcross breeding lines (BC 2F 5) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC 2F 3 and BC 2F 4 generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC 2F 5 generation whereas 29 QTLs were detected in BC 2F 2 generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R 2 values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC 2F 5 population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.",
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AU - Bhuiyan, M. A R

AU - Kalluvettankuzhy, Sabu K.

AU - Lim, Li Sze

AU - Thomson, Michael J.

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AU - Abdullah, Md Zain

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