scholarly journals Whole‐genome resequencing‐based QTL ‐seq identified AhTc1 gene encoding a R2R3‐ MYB transcription factor controlling peanut purple testa colour

2019 ◽  
Vol 18 (1) ◽  
pp. 96-105 ◽  
Author(s):  
Yuhan Zhao ◽  
Junjie Ma ◽  
Ming Li ◽  
Li Deng ◽  
Guanghui Li ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Myb Transcription Factor ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Gene Encoding ◽  
Whole Genome Resequencing ◽  
R2r3 Myb ◽  
Testa Colour

scholarly journals A single nucleotide polymorphism in an R2R3 MYB transcription factor gene triggers the male sterility in soybean ms6 (Ames1)

2021 ◽  
Author(s):  
Junping Yu ◽  
Guolong Zhao ◽  
Wei Li ◽  
Ying Zhang ◽  
Peng Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Glycine Max ◽  
Male Sterility ◽  
Bulked Segregant Analysis ◽  
Soybean Protein ◽  
Anther Development ◽  
Hybrid Breeding ◽  
Myb Transcription Factor ◽  
Male Sterile ◽  
R2r3 Myb

Abstract Key message Identification and functional analysis of the male sterile gene MS6 in Glycine max. Abstract Soybean (Glycine max (L.) Merr.) is an important crop providing vegetable oil and protein. The male sterility-based hybrid breeding is a promising method for improving soybean yield to meet the globally growing demand. In this research, we identified a soybean genic male sterile locus, MS6, by combining the bulked segregant analysis sequencing method and the map-based cloning technology. MS6, highly expressed in anther, encodes an R2R3 MYB transcription factor (GmTDF1-1) that is homologous to Tapetal Development and Function 1, a key factor for anther development in Arabidopsis and rice. In male sterile ms6 (Ames1), the mutant allele contains a missense mutation, leading to the 76th leucine substituted by histidine in the DNA binding domain of GmTDF1-1. The expression of soybean MS6 under the control of the AtTDF1 promoter could rescue the male sterility of attdf1 but ms6 could not. Additionally, ms6 overexpression in wild-type Arabidopsis did not affect anther development. These results evidence that GmTDF1-1 is a functional TDF1 homolog and L76H disrupts its function. Notably, GmTDF1-1 shows 92% sequence identity with another soybean protein termed as GmTDF1-2, whose active expression also restored the fertility of attdf1. However, GmTDF1-2 is constitutively expressed at a very low level in soybean, and therefore, not able to compensate for the MS6 deficiency. Analysis of the TDF1-involved anther development regulatory pathway showed that expressions of the genes downstream of TDF1 are significantly suppressed in ms6, unveiling that GmTDF1-1 is a core transcription factor regulating soybean anther development.

scholarly journals Whole genome resequencing and custom genotyping unveil clonal lineages in ‘Malbec’ grapevines (Vitis vinifera L.)

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Luciano Calderón ◽  
Nuria Mauri ◽  
Claudio Muñoz ◽  
Pablo Carbonell-Bejerano ◽  
Laura Bree ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Somatic Mutations ◽  
Clonal Propagation ◽  
Variant Calling ◽  
Vitis Vinifera L ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Genome Resequencing ◽  
Diversity Pattern ◽  
Whole Genome Resequencing

AbstractGrapevine cultivars are clonally propagated to preserve their varietal attributes. However, genetic variations accumulate due to the occurrence of somatic mutations. This process is anthropically influenced through plant transportation, clonal propagation and selection. Malbec is a cultivar that is well-appreciated for the elaboration of red wine. It originated in Southwestern France and was introduced in Argentina during the 1850s. In order to study the clonal genetic diversity of Malbec grapevines, we generated whole-genome resequencing data for four accessions with different clonal propagation records. A stringent variant calling procedure was established to identify reliable polymorphisms among the analyzed accessions. The latter procedure retrieved 941 single nucleotide variants (SNVs). A reduced set of the detected SNVs was corroborated through Sanger sequencing, and employed to custom-design a genotyping experiment. We successfully genotyped 214 Malbec accessions using 41 SNVs, and identified 14 genotypes that clustered in two genetically divergent clonal lineages. These lineages were associated with the time span of clonal propagation of the analyzed accessions in Argentina and Europe. Our results show the usefulness of this approach for the study of the scarce intra-cultivar genetic diversity in grapevines. We also provide evidence on how human actions might have driven the accumulation of different somatic mutations, ultimately shaping the Malbec genetic diversity pattern.

scholarly journals Different Mechanisms Participate in the R-dependent Activity of the R2R3 MYB Transcription Factor C1

2004 ◽  
Vol 279 (46) ◽  
pp. 48205-48213 ◽  
Author(s):  
J. Marcela Hernandez ◽  
George F. Heine ◽  
Niloufer G. Irani ◽  
Antje Feller ◽  
Min-Gab Kim ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Myb Transcription Factor ◽  
Dependent Activity ◽  
R2r3 Myb
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