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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: 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.The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s.

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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Comparison of genomic sequences and amino acid sequences of rice qPPB3 between two parents. a The qPPB3 gene is composed of three exons and two introns. Black and white boxes indicate coding and untranslated region (UTR), respectively, and lines represent introns. Arrows indicate the locations of the 93-11 mutation. b The nucleotide substitution for change of amino acid is marked with a red box. c Multiple deduced amino acid sequence alignment of protein coded by qPPB3 of Nipponbare, 93-11, and PA64s. A red box indicates the altered amino acid
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Fig3: Comparison of genomic sequences and amino acid sequences of rice qPPB3 between two parents. a The qPPB3 gene is composed of three exons and two introns. Black and white boxes indicate coding and untranslated region (UTR), respectively, and lines represent introns. Arrows indicate the locations of the 93-11 mutation. b The nucleotide substitution for change of amino acid is marked with a red box. c Multiple deduced amino acid sequence alignment of protein coded by qPPB3 of Nipponbare, 93-11, and PA64s. A red box indicates the altered amino acid

Mentions: To screen candidate genes in the critical 34.6-kb genomic region of Nipponbare genome (http://rapdb.dna.affrc.go.jp/), and four corresponding genes (Os03g0203100, Os03g0203200, Os03g0203700, Os03g0203800) were found. After comparing sequence of the region between parents, only two genes, Os03g0203200 and Os03g0203700, had three SNPs and one InDel between two parents, respectively. However, product of Os03g0203700 was similar to Calcium-transporting ATPase 2, which has been found irrelevant to plant branching so far, and its expression showed no significant difference between two parents. Instead, Os03g0203200 (D88) encoded esterase D14/D88 homologous to the α/β-fold hydrolase superfamily protein, which has been reported affecting plant branching and significant difference in its expression level was detected here between 93-11 and PA64s. Only one substitution (T959 to G959) resulted in amino acid change from valine in 93-11 to glycine in PA64s (Fig. 3). Therefore, Os03g0203200 (D88) gene was suggested to be a candidate gene for qPPB3.Fig. 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)

Comparison of genomic sequences and amino acid sequences of rice qPPB3 between two parents. a The qPPB3 gene is composed of three exons and two introns. Black and white boxes indicate coding and untranslated region (UTR), respectively, and lines represent introns. Arrows indicate the locations of the 93-11 mutation. b The nucleotide substitution for change of amino acid is marked with a red box. c Multiple deduced amino acid sequence alignment of protein coded by qPPB3 of Nipponbare, 93-11, and PA64s. A red box indicates the altered amino acid
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4197378&req=5

Fig3: Comparison of genomic sequences and amino acid sequences of rice qPPB3 between two parents. a The qPPB3 gene is composed of three exons and two introns. Black and white boxes indicate coding and untranslated region (UTR), respectively, and lines represent introns. Arrows indicate the locations of the 93-11 mutation. b The nucleotide substitution for change of amino acid is marked with a red box. c Multiple deduced amino acid sequence alignment of protein coded by qPPB3 of Nipponbare, 93-11, and PA64s. A red box indicates the altered amino acid
Mentions: To screen candidate genes in the critical 34.6-kb genomic region of Nipponbare genome (http://rapdb.dna.affrc.go.jp/), and four corresponding genes (Os03g0203100, Os03g0203200, Os03g0203700, Os03g0203800) were found. After comparing sequence of the region between parents, only two genes, Os03g0203200 and Os03g0203700, had three SNPs and one InDel between two parents, respectively. However, product of Os03g0203700 was similar to Calcium-transporting ATPase 2, which has been found irrelevant to plant branching so far, and its expression showed no significant difference between two parents. Instead, Os03g0203200 (D88) encoded esterase D14/D88 homologous to the α/β-fold hydrolase superfamily protein, which has been reported affecting plant branching and significant difference in its expression level was detected here between 93-11 and PA64s. Only one substitution (T959 to G959) resulted in amino acid change from valine in 93-11 to glycine in PA64s (Fig. 3). Therefore, Os03g0203200 (D88) gene was suggested to be a candidate gene for qPPB3.Fig. 3

Bottom Line: 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.The expression of APO1 and IPA1 increased, while GN1a and DST decreased in 93-11 compared with PA64s.

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