miR156f integrates panicle architecture through genetic modulation of branch number and pedicel length pathways

Abstract Background The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total of 421 purified, homozygous rice accessions representing diverse genetic variations within O. sativa. The release of High-Density Rice Array (HDRA, 700 k SNPs) dataset provides a new opportunity to discover the genetic variants of panicle architectures in rice. Results In this report, a new method genome-phenome wide association study (GPWAS) was performed with 391 individuals and 27 traits derived from RDP1 to scan the relationship between the genes and multi-traits. A total of 1985 gene models were linked to phenomic variation with a p-value cutoff of 4.49E-18. Besides, 406 accessions derived from RDP1 with 411,066 SNPs were used to identify QTLs associated with the total spikelets number per panicle (TSNP), grain number per panicle (GNP), empty grain number per panicle (EGNP), primary branch number (PBN), panicle length (PL), and panicle number per plant (PN) by GLM, MLM, FarmCPU, and BLINK models for genome-wide association study (GWAS) analyses. A total of 18, 21, 18, 17, 15, and 17 QTLs were identified tightly linked with TSNP, GNP, EGNP, PBN, PL, and PN, respectively. Then, a total of 23 candidate genes were mapped simultaneously using both GWAS and GPWAS methods, composed of 6, 4, 5, 4, and 4 for TSNP, GNP, EGNP, PBN, and PL. Notably, one overlapped gene (Os01g0140100) were further investigated based on the haplotype and gene expression profile, indicating this gene might regulate the TSNP or panicle architecture in rice. Conclusions Nearly 30 % (30/106) QTLs co-located with the previous published genes or QTLs, indicating the power of GWAS. Besides, GPWAS is a new method to discover the relationship between genes and traits, especially the pleiotropy genes. Through comparing the results from GWAS and GPWAS, we identified 23 candidate genes related to panicle architectures in rice. This comprehensive study provides new insights into the genetic basis controlling panicle architectures in rice, which lays a foundation in rice improvement.

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Major Quantitative Trait Loci Mapping for Tassel Branch Number and Construction of qTBN5 Near-isogenic Lines in Maize (Zea mays L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2018.01127 ◽

2018 ◽

Vol 44 (8) ◽

pp. 1127

Author(s):

Zi-Ju DAI ◽

Xin-Tao WANG ◽

Qing YANG ◽

Yan WANG ◽

Ying-Ying ZHANG ◽

...

Keyword(s):

Zea Mays ◽

Quantitative Trait Loci ◽

Quantitative Trait ◽

Zea Mays L ◽

Quantitative Trait Loci Mapping ◽

Near Isogenic Lines ◽

Branch Number ◽

Isogenic Lines ◽

Tassel Branch Number ◽

Trait Loci

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Registration of two Oryza sativa tropical japonica germplasm lines selected for panicle architecture and grain size traits

Journal of Plant Registrations ◽

10.1002/plr2.20145 ◽

2021 ◽

Author(s):

Georgia C. Eizenga ◽

Anna M. McClung ◽

Trevis D. Huggins

Keyword(s):

Grain Size ◽

Oryza Sativa ◽

Tropical Japonica ◽

Panicle Architecture

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Q Dtbn1 , an F‐box gene affecting maize tassel branch number by a dominant model

Plant Biotechnology Journal ◽

10.1111/pbi.13540 ◽

2020 ◽

Author(s):

Xiner Qin ◽

Shike Tian ◽

Wenliang Zhang ◽

Xue Dong ◽

Chengxin Ma ◽

...

Keyword(s):

Dominant Model ◽

Branch Number ◽

Maize Tassel ◽

Tassel Branch Number

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Estimation of Genetic Parameters and Wood Yield Selection Index in a Clonal Trial of Korean Pine (Pinus koraiensis) in Northeastern China

Sustainability ◽

10.3390/su13084167 ◽

2021 ◽

Vol 13 (8) ◽

pp. 4167

Author(s):

David Kombi Kaviriri ◽

Huan-Zhen Liu ◽

Xi-Yang Zhao

Keyword(s):

Selection Index ◽

Tree Height ◽

Stem Volume ◽

Korean Pine ◽

Branch Number ◽

Basal Diameter ◽

Diameter At Breast Height ◽

Breast Height ◽

Stem Straightness ◽

Clonal Trial

In order to determine suitable traits for selecting high-wood-yield Korean pine materials, eleven morphological characteristics (tree height, basal diameter, diameter at breast height, diameter at 3 meter height, stem straightness degree, crown breadth, crown height, branch angle, branch number per node, bark thickness, and stem volume) were investigated in a 38-year-old Korean pine clonal trial at Naozhi orchard. A statistical approach combining variance and regression analysis was used to extract appropriate traits for selecting elite clones. Results of variance analysis showed significant difference in variance sources in most of the traits, except for the stem straightness degree, which had a p-value of 0.94. Moderate to high coefficients of variation and clonal repeatability ranged from 10.73% to 35.45% and from 0.06% to 0.78%, respectively. Strong significant correlations on the phenotypic and genotypic levels were observed between the straightness traits and tree volume, but crown breadth was weakly correlated to the volume. Four principal components retaining up to 80% of the total variation were extracted, and stem volume, basal diameter, diameter at breast height, diameter at 3 meter height, tree height, and crown height displayed high correlation to these components (r ranged from 0.76 to 0.98). Based on the Type III sum of squares, tree height, diameter at breast height, and branch number showed significant information to explain the clonal variability based on stem volume. Using the extracted characteristics as the selection index, six clones (PK105, PK59, PK104, PK36, PK28, and K101) displayed the highest Qi values, with a selection rate of 5% corresponding to the genetic gain of 42.96% in stem volume. This study provides beneficial information for the selection of multiple traits for genetically improved genotypes of Korean pine.

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Correction to: Genome-wide association study to identify chromosomal regions related to panicle architecture in rice (Oryza spp.)

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01185-6 ◽

2021 ◽

Author(s):

Ranjita Thapa ◽

Rodante E. Tabien ◽

Endang M. Septiningsih

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

Panicle Architecture

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Responses of Branch Number and Yield Component of Soybean Cultivars Tested in Different Planting Densities

Agriculture ◽

10.3390/agriculture11010069 ◽

2021 ◽

Vol 11 (1) ◽

pp. 69

Author(s):

Cailong Xu ◽

Ruidong Li ◽

Wenwen Song ◽

Tingting Wu ◽

Shi Sun ◽

...

Keyword(s):

Key Management ◽

Management Practices ◽

Yield Component ◽

Planting Density ◽

Yield Potential ◽

High Yield ◽

Branch Number ◽

Soybean Yield ◽

Soybean Cultivars ◽

Pod Number

Increasing planting density is one of the key management practices to enhance soybean yield. A 2-yr field experiment was conducted in 2018 and 2019 including six planting densities and two soybean cultivars to determine the effects of planting density on branch number and yield, and analyze the contribution of branches to yield. The yield of ZZXA12938 was 4389 kg ha−1, which was significantly higher than that of ZH13 (+22.4%). In combination with planting year and cultivar, the soybean yield increased significantly by 16.2%, 31.4%, 41.4%, and 46.7% for every increase in density of 45,000 plants ha−1. Yield will not increase when planting density exceeds 315,000 plants ha−1. A correlation analysis showed that pod number per plant increased with the increased branch number, while pod number per unit area decreased; thus, soybean yield decreased. With the increase of branch number, the branch contribution to yield increased first, and then plateaued. ZH13 could produce a high yield under a lower planting density due to more branches, while ZZXA12938 had a higher yield potential under a higher planting density due to the smaller branch number and higher tolerance to close planting. Therefore, seed yield can be increased by selecting cultivars with a little branching capacity under moderately close planting.

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