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Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice.

Peng Y, Gao Z, Zhang B, Liu C, Xu J, Ruan B, Hu J, Dong G, Guo L, Liang G, Qian Q - Plant Cell Rep. (2014)

Bottom Line: The T to G substitution resulted in one amino acid change from valine in 93-11 to glycine in PA64s.The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s.Therefore, D88/D14 is not only a key regulator for branching, but also affects panicle structure.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology College of Agriculture, Yangzhou University, Yangzhou, 225009, China, youlinp@hotmail.com.

ABSTRACT

Key message: A gene not only control tiller and plant height, but also regulate panicle structure by QTL dissection in rice. An ideal panicle structure is important for improvement of plant architecture and rice yield. In this study, using recombinant inbred lines (RILs) of PA64s and 93-11, we identified a quantitative trait locus (QTL), designated qPPB3 for primary panicle branch number. With a BC3F2 population derived from a backcross between a resequenced RIL carrying PA64s allele and 93-11, qPPB3 was fine mapped to a 34.6-kb genomic region. Gene prediction analysis identified four putative genes, among which Os03g0203200, a previously reported gene for plant height and tiller number, Dwarf 88 (D88)/Dwarf 14 (D14), had three nucleotide substitutions in 93-11 compared with PA64s. The T to G substitution resulted in one amino acid change from valine in 93-11 to glycine in PA64s. Real-time PCR analysis showed expression level of D88 was higher in 93-11 than PA64s. The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s. Therefore, D88/D14 is not only a key regulator for branching, but also affects panicle structure.

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Related in: MedlinePlus

a QTLs for panicle traits in the RIL population. SNP markers are shown on the left of chromosomes. QTLs signed on chromosomes were detected in several environments and different years. b QTL peak map of rice chromosome 3. The genetic distances (cM) are shown below the x axis. c Fine mapping of qPPB3. The white, black, and graybars represent genotypes of PA64s, 93-11, and heterozygote, respectively. All genotypic lines exhibited (G1-G11) were derived from BC3F2 population
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Fig2: a QTLs for panicle traits in the RIL population. SNP markers are shown on the left of chromosomes. QTLs signed on chromosomes were detected in several environments and different years. b QTL peak map of rice chromosome 3. The genetic distances (cM) are shown below the x axis. c Fine mapping of qPPB3. The white, black, and graybars represent genotypes of PA64s, 93-11, and heterozygote, respectively. All genotypic lines exhibited (G1-G11) were derived from BC3F2 population

Mentions: QTL analysis was performed with MultiQTL1.6 using the maximum likelihood interval mapping approach with an LOD threshold 2.5. We detected two QTLs for PPB on chromosomes 3 and 8, named qPPB3 and qPPB8. The qPPB3 explained 9.4 % phenotypic variation with additive effect came from PA64s. And qPPB8 explained 15.3 % phenotypic variation came from 93-11. Two QTLs for SPB were identified. The qSPB1 was mapped on chromosome 1 and explained 10 % phenotypic variation with additive effect came from 93-11. The positive effect of qSPB9 was from 93-11, explained 9.6 % phenotypic variation. PPB and SPB are two key factors for SN determined by panicle architecture. Two QTLs, qSN8 and qSN9 for SN were mapped on chromosomes 8 and 9 with additive effects of 35.5 and 33.2, respectively (Table 3; Fig. 2a). They totally explained 25.4 % phenotypic variation.Table 3


Fine mapping and candidate gene analysis of a major QTL for panicle structure in rice.

Peng Y, Gao Z, Zhang B, Liu C, Xu J, Ruan B, Hu J, Dong G, Guo L, Liang G, Qian Q - Plant Cell Rep. (2014)

a QTLs for panicle traits in the RIL population. SNP markers are shown on the left of chromosomes. QTLs signed on chromosomes were detected in several environments and different years. b QTL peak map of rice chromosome 3. The genetic distances (cM) are shown below the x axis. c Fine mapping of qPPB3. The white, black, and graybars represent genotypes of PA64s, 93-11, and heterozygote, respectively. All genotypic lines exhibited (G1-G11) were derived from BC3F2 population
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4197378&req=5

Fig2: a QTLs for panicle traits in the RIL population. SNP markers are shown on the left of chromosomes. QTLs signed on chromosomes were detected in several environments and different years. b QTL peak map of rice chromosome 3. The genetic distances (cM) are shown below the x axis. c Fine mapping of qPPB3. The white, black, and graybars represent genotypes of PA64s, 93-11, and heterozygote, respectively. All genotypic lines exhibited (G1-G11) were derived from BC3F2 population
Mentions: QTL analysis was performed with MultiQTL1.6 using the maximum likelihood interval mapping approach with an LOD threshold 2.5. We detected two QTLs for PPB on chromosomes 3 and 8, named qPPB3 and qPPB8. The qPPB3 explained 9.4 % phenotypic variation with additive effect came from PA64s. And qPPB8 explained 15.3 % phenotypic variation came from 93-11. Two QTLs for SPB were identified. The qSPB1 was mapped on chromosome 1 and explained 10 % phenotypic variation with additive effect came from 93-11. The positive effect of qSPB9 was from 93-11, explained 9.6 % phenotypic variation. PPB and SPB are two key factors for SN determined by panicle architecture. Two QTLs, qSN8 and qSN9 for SN were mapped on chromosomes 8 and 9 with additive effects of 35.5 and 33.2, respectively (Table 3; Fig. 2a). They totally explained 25.4 % phenotypic variation.Table 3

Bottom Line: The T to G substitution resulted in one amino acid change from valine in 93-11 to glycine in PA64s.The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s.Therefore, D88/D14 is not only a key regulator for branching, but also affects panicle structure.

View Article: PubMed Central - PubMed

Affiliation: Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genetics and Physiology College of Agriculture, Yangzhou University, Yangzhou, 225009, China, youlinp@hotmail.com.

ABSTRACT

Key message: A gene not only control tiller and plant height, but also regulate panicle structure by QTL dissection in rice. An ideal panicle structure is important for improvement of plant architecture and rice yield. In this study, using recombinant inbred lines (RILs) of PA64s and 93-11, we identified a quantitative trait locus (QTL), designated qPPB3 for primary panicle branch number. With a BC3F2 population derived from a backcross between a resequenced RIL carrying PA64s allele and 93-11, qPPB3 was fine mapped to a 34.6-kb genomic region. Gene prediction analysis identified four putative genes, among which Os03g0203200, a previously reported gene for plant height and tiller number, Dwarf 88 (D88)/Dwarf 14 (D14), had three nucleotide substitutions in 93-11 compared with PA64s. The T to G substitution resulted in one amino acid change from valine in 93-11 to glycine in PA64s. Real-time PCR analysis showed expression level of D88 was higher in 93-11 than PA64s. The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s. Therefore, D88/D14 is not only a key regulator for branching, but also affects panicle structure.

Show MeSH
Related in: MedlinePlus