Panicle Architecture In Rice Research Articles

Analisis Genetik Arsitektur Malai Padi Menggunakan Dua Populasi F2

<em>Improvement of rice panicle architecture is one important objective in the development of improved new-plant-type rice varieties. Panicle architecture is directly related to yield components in rice. The aims of this study were to obtain information on inheritance pattern of panicle architecture on F2 generation and to obtain the best selected individuals. The experiment was conducted at Sawah Baru Experimental Farm Bogor, from May to October 2016. Two F2 populations derived from crosses of IPB 3S/IPB160-F-36, IPB160-F-36/IPB 5R and three genotypes of parents were used as experimental materials. A total of 208 and 204 plant samples were taken representing each of the two F2 populations and 20 plants representing the parents. Three panicles were taken randomly from each individual as observed samples. The results showed that additive gene action influenced number of primary branches in population of IPB 3S/IPB160-F-36, whereas in the population of IPB160-F-36/IPB 5R, most of the panicle architecture traits were controlled by additive gene action except for the length of primary branches. All of panicle architecture traits were controlled by relatively many genes except length of primary branches and number of grains on primary branches in the IPB 3S/IPB160-F-36 population. The panicle architecture of the two observed population was genetically varies. The heritability estimates were moderate to high. Selection could increase the mean of panicle architecture traits using either single or multiple traits simultaneously.<br /><br />Keywords: gene action, heritability, genetic variability, panicle traits <br /><br /></em>

MiR529a modulates panicle architecture through regulating SQUAMOSA PROMOTER BINDING-LIKE genes in rice (Oryza sativa).

MiR529a affects rice panicle architecture by targeting OsSPL2,OsSPL14 and OsSPL17 genes that could regulate their downstream panicle related genes. The panicle architecture determines the grain yield and quality of rice, which could be regulated by many transcriptional factors. The SQUAMOSA PROMOTER BINDING-LIKE (SPL) transcription factors are involved in the regulation of panicle development, which are targeted by miR156 and miR529. The expression profile demonstrated that miR529a is preferentially expressed in the early panicle of rice and it might regulate panicle development in rice. However, the regulation mechanism of miR529-SPL is still not clear. In this study, we predicted five miR529a putative target genes, OsSPL2, OsSPL14, OsSPL16, OsSPL17 and OsSPL18, while only the expression of OsSPL2, OsSPL14, and OsSPL17 was regulated by miR529a in the rice panicle. Overexpression of miR529a dramatically affected panicle architecture, which was regulated by OsSPL2, OsSPL14, and OsSPL17. Furthermore, the 117, 35, and 25 pathway genes associated with OsSPL2, OsSPL14 and OsSPL17, respectively, were predicted, and they shared 20 putative pathway genes. Our results revealed that miR529a could play a vital role in the regulation of panicle architecture through regulating OsSPL2, OsSPL14, OsSPL17 and the complex networks formed by their pathway and downstream genes. These findings will provide new genetic resources for reshaping ideal plant architecture and breeding high yield rice varieties.

イネNested association mapping集団による穂の着粒構造に関するQTL同定

イネNested association mapping集団による穂の着粒構造に関するQTL同定

Genome‐Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between Indica and Japonica Rice

Panicle architecture determines the number of spikelets per panicle (SPP) and is highly associated with grain yield in rice ( L.). Understanding the genetic basis of panicle architecture is important for improving the yield of rice grain. In this study, we dissected panicle architecture traits into eight components, which were phenotyped from a germplasm collection of 529 cultivars. Multiple regression analysis revealed that the number of secondary branch (NSB) was the major factor that contributed to SPP. Genome-wide association analysis was performed independently for the eight particle architecture traits observed in the and rice subpopulations compared with the whole rice population. In total, 30 loci were associated with these traits. Of these, 13 loci were closely linked to known panicle architecture genes, and 17 novel loci were repeatedly identified in different environments. An association signal cluster was identified for NSB and number of spikelets per secondary branch (NSSB) in the region of 31.6 to 31.7 Mb on chromosome 4. In addition to the common associations detected in both and subpopulations, many associated loci were unique to one subpopulation. For example, and were specifically associated with panicle length (PL) in and rice, respectively. Moreover, the -mediated flowering genes and were associated with the formation of panicle architecture in rice. These results suggest that different gene networks regulate panicle architecture in and rice.

Variations in DENSE AND ERECT PANICLE 1 (DEP1) contribute to the diversity of the panicle trait in high-yielding japonica rice varieties in northern China.

Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense and erect panicle 1 (DEP1) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. We further detected 7 haplotypes and found that the replacement of 637 bp by a 12 bp fragment could explain the erect panicle architecture in all 72 germplasms. An SNP (G/C) at the -1253 bp of the promoter region caused a core sequence shift (TGGGCC) of a site II transcriptional regulatory element. The association analysis showed that the SNP(G/C) largely affects the number of primary and secondary branches, and grain number per panicle. Our results provide novel insights into the function and genetic diversity of DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding.

Quantitative trait locus analysis and fine mapping of the qPL6 locus for panicle length in rice.

Two QTLs were identified to control panicle length in rice backcross lines, and one QTL qPL6 was finely mapped with potential in high yield breeding. Panicle length (PL) is the key determinant of panicle architecture in rice, and strongly affects yield components, such as grain number per panicle. However, this trait has not been well studied genetically nor its contribution to yield improvement. In this study, we performed quantitative trait locus (QTL) analysis for PL in four backcross populations derived from the cross of Nipponbare (japonica) and WS3 (indica), a new plant type (NPT) variety. Two QTLs were identified on chromosome 6 and 8, designated as qPL6 and qPL8, respectively. Near-isogenic lines (NILs) were developed to evaluate their contribution to important agronomic traits. We found that qPL6 and qPL8 had additive effects on PL trait. For the qPL6 locus, the WS3 allele also increased panicle primary and secondary branches and grain number per panicle. Moreover, this allele conferred wide and strong culms, a character of lodging resistance. By analyzing key recombinants in two steps, the qPL6 locus was finely mapped to a 25-kb interval, and 3 candidate genes were identified. According to the single nucleotide polymorphisms (SNPs) within candidate genes, 5 dCaps markers were designed and used to get haplotypes of 96 modern Chinese varieties, which proved that qPL6 locus is differentiated between indica and temperate japonica varieties. Taken together, the superior qPL6 allele can be applied in rice breeding programs for large sink size, particularly for japonica varieties that originally lack the allele.

Fine mapping and candidate gene analysis of a new mutant gene for panicle apical abortion in rice

The rice panicle architecture depends on the arrangement of branches and spikelets which directly affect grain yield. We identified a mutant for panicle apical abortion (PAA-Hwa) from a japonica cultivar Hwacheongbyeo treated with N-methyl-N-nitrosourea. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as a slight reduction in plant height, narrow and dark green leaf blades, and small erect panicles with clear PAA compared to the wild-type plants. Genetic analysis revealed that the PAA was controlled by a single recessive gene, which is tentatively designated as paa-h. The paa-h gene was fine mapped at an interval of 71 kb flanked by sequence tagged site markers aptn3 and S6685-1 at the long arm of chromosome 4. Sequence analysis of the candidate genes within the delimited region showed a single base-pair change corresponding to an amino acid substitution from glycine to glutamic acid at the candidate gene, LOC_Os04g56160. We expect that the paa-h gene will be a clue to uncover the molecular mechanism of PAA and to maintain the panicle identity for grain yield in rice breeding programs.

A novel frameshift mutant allele, fzp-10, affecting the panicle architecture of rice

The rice FRIZZY PANICLE (FZP) locus on chromosome 7, in which an ERF and acidic domain are present, is concerned with the regulation of spikelet meristem identity and the determination of panicle architecture. Many fzp mutants drastically alter panicle morphology with higher-order rachis-branches developing successively instead of the development of floral organs in these mutants. A new mutant showing the same fzp phenotype was induced by γ-ray irradiation of seeds of a rice cultivar “Gimbozu”. Examination of this fzp-like mutant for its allelism to a known allele of fzp-1, nucleotide sequence, and panicle and agronomic characteristics clearly indicated that the allele of this fzp-like mutant is located in FZP. Because there is a previously identified allele called fzp-9, we designated this new allele as fzp-10. fzp-10 has a single nucleotide (cytosine) deletion between the ERF domain and the acidic domain, which results in a frameshift mutation and a premature stop codon, thereby altering the C-terminus of the encoded protein. The degree of higher-order branching in the panicles was significantly reduced in the fzp-10 mutant compared with that of fzp-1. Moreover, the fzp-10 mutant showed highly depressed culm and panicle lengths and panicle number, as well as delayed heading dates compared with its wild type and also with fzp-1. fzp-10 has several new characteristics, its altered nucleotide position and severity of phenotype alteration, and, therefore, could be a new gene resource to examine the function of FZP and the determination of rice panicle architecture.

Map-based cloning of the ERECT PANICLE 3 gene in rice

Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.

Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice

To understand the genetic basis of yield-related traits of rice, we developed 39 chromosome segment substitution lines (CSSLs) from a cross between an average-yielding japonica cultivar, Sasanishiki, as the recurrent parent and a high-yielding indica cultivar, Habataki, as the donor. Five morphological components of panicle architecture in the CSSLs were evaluated in 2 years, and 38 quantitative trait loci (QTLs) distributed on 11 chromosomes were detected. The additive effect of each QTL was relatively small, suggesting that none of the QTLs could explain much of the phenotypic difference in sink size between Sasanishiki and Habataki. We developed nearly isogenic lines for two major QTLs, qSBN1 (for secondary branch number on chromosome 1) and qPBN6 (for primary branch number on chromosome 6), and a line containing both. Phenotypic analysis of these lines revealed that qSBN1 and qPBN6 contributed independently to sink size and that the combined line produced more spikelets. This suggests that the cumulative effects of QTLs distributed throughout the genome form the major genetic basis of panicle architecture in rice.

Genetic analysis and fine mapping of a lax mutant in rice

We have analyzed a lax mutant that exhibits altered panicle architecture in rice. The primary and secondary rachis-branches are normally initiated and each branch ends in a terminal spikelet, but all the lateral spikelets are absent and the terminal spikelet displays variegated structures in the mutant. An F2 population from the cross between the lax mutant and a japonica variety, W11, was constructed and analyzed. Using microsatellite and CAPS markers, the lax locus was mapped on the long arm of chromosome 1, co-segregated with a CAPS marker, LZ1, within an interval of 0.28 cM between a CAPS marker, HB2, and a microsatellite marker, MRG4389. RT-PCR analysis revealed that the expressions of the rice B-function MADS-box genes OsMADS2, OsMADS4, OsMADS16 and OsMADS3 were significantly reduced, whereas the expression of the rice A-function gene RAP1A was not altered.

The LAX1 and FRIZZY PANICLE 2 Genes Determine the Inflorescence Architecture of Rice by Controlling Rachis-Branch and Spikelet Development

We have analyzed two mutants that exhibit altered panicle architecture in rice (Oryza sativa L.). In lax1-2, which is a new and stronger allele of the previously reported lax mutant, initiation and/or maintenance of rachis-branches, lateral spikelets, and terminal spikelets was severely prevented. In situ hybridization analysis using OSH1, a rice knotted1 (kn1) ortholog, confirmed the absence of lateral meristems in lax1-2 panicles. These defects indicate that the LAX1 gene is required for the initiation/maintenance of axillary meristems in the rice panicle. In addition to its role in forming lateral meristems, the wild-type LAX1 gene acts as a floral meristem identity gene which specifies the terminal spikelet meristem. A comparison of the defects in lax1-1 and lax1-2 plants suggested that the sensitivities to reduced LAX1 activity were not uniform among different types of meristems. In the fzp2 mutant panicle, the basic branching pattern of the panicle was indistinguishable from that of the wild type; however, specification of both terminal and lateral spikelet meristems was blocked, and sequential rounds of branching occurred at the point where the spikelet meristems are initiated in the wild-type panicle. This resulted in the generation of a panicle composed of excessive ramification of rachis-branches. The lax1-1 fzp2 double mutants exhibited a novel, basically additive, phenotype, which suggests that LAX1 and FZP2 function in genetically independent pathways.