A naturally occurring InDel variation in BraA.FLC.b (BrFLC2) associated with flowering time variation in Brassica rapa

Abstract Previous QTL mapping identified a Brassica nigra homolog to Arabidopsis thaliana CO as a candidate gene affecting flowering time in B. nigra. Transformation of an A. thaliana co mutant with two different alleles of the B. nigra CO (Bni COa) homolog, one from an early-flowering B. nigra plant and one from a late one, did not show any differential effect of the two alleles on flowering time. The DNA sequence of the coding region of the two alleles was also identical, showing that nucleotide variation influencing flowering time must reside outside the coding region of Bni COa. In contrast, the nucleotide sequence of the B. nigra COL1 (Bni COL1) gene located 3.5 kb upstream of Bni COa was highly diverged between the alleles from early and late plants. One indel polymorphism in the Bni COL1 coding region, present in several natural populations of B. nigra, displayed a significant association with flowering time within a majority of these populations. These data indicate that a quantitative trait nucleotide (QTN) affecting flowering time is located within or close to the Bni COL1 gene. The intergenic sequence between Bni COL1 and Bni COa displayed a prominent peak of divergence 1 kb downstream of the Bni COL1 coding region. This region could contain regulatory elements for the downstream Bni COa gene. Our data suggest that a naturally occurring QTN for flowering time affects the function or expression of either Bni COL1 or Bni COa.

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Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

Genome ◽

10.1139/g10-082 ◽

2010 ◽

Vol 53 (11) ◽

pp. 884-898 ◽

Cited By ~ 31

Author(s):

Jianjun Zhao ◽

Anna Artemyeva ◽

Dunia Pino Del Carpio ◽

Ram Kumar Basnet ◽

Ningwen Zhang ◽

...

Keyword(s):

Association Mapping ◽

Flowering Time ◽

Brassica Rapa ◽

Core Collection ◽

Field Experiments ◽

Research Centre ◽

Candidate Gene Approach ◽

Core Collections ◽

Genome Wide ◽

Using Data

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

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Vernalization can regulate flowering time through microRNA mechanism in Brassica rapa

Physiologia Plantarum ◽

10.1111/ppl.12692 ◽

2018 ◽

Vol 164 (2) ◽

pp. 204-215 ◽

Cited By ~ 3

Author(s):

Feiyi Huang ◽

Xiaoting Wu ◽

Xilin Hou ◽

Shuaixu Shao ◽

Tongkun Liu

Keyword(s):

Flowering Time ◽

Brassica Rapa

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The Molecular Genetic Basis of Flowering Time Variation in Brassica Species

Biotechnology in Agriculture and Forestry - Brassicas and Legumes From Genome Structure to Breeding ◽

10.1007/978-3-662-05036-1_5 ◽

2003 ◽

pp. 69-86 ◽

Cited By ~ 9

Author(s):

T. C. Osborn ◽

L. Lukens

Keyword(s):

Flowering Time ◽

Time Variation ◽

Genetic Basis ◽

Molecular Genetic ◽

Brassica Species ◽

Molecular Genetic Basis

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BBX32 Interacts with AGL24 Involved in Flowering Time Control in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha47111205 ◽

2018 ◽

Vol 47 (1) ◽

pp. 34-45

Author(s):

Guan-Peng MA ◽

Da-Qin ZHAO ◽

Tian-Wen WANG ◽

Lin-Bi ZHOU ◽

Gui-Lian LI

Keyword(s):

Arabidopsis Thaliana ◽

Circadian Clock ◽

Flowering Time ◽

Brassica Rapa ◽

Chinese Cabbage ◽

Protein Interactions ◽

Protein Protein Interactions ◽

Time Control ◽

Flowering Time Control ◽

Molecular Regulatory Mechanisms

B-box (BBX) zinc finger proteins play critical roles in both vegetative and reproductive development in plants. Many BBX proteins have been identified in Arabidopsis thaliana as floral transition regulatory factors, such as CO, BBX7 (COL9), BBX19, and BBX32. BBX32 is involved in flowering time control through repression of COL3 in Arabidopsis thaliana, but it is still elusive that whether and how BBX32 directly interacts with flowering signal integrators of AGAMOUS-LIKE 24 (AGL24) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) in Chinese cabbage (Brassica rapa L. ssp. pekinensis) or other plants. In this study, B-box-32(BBX32), a transcription factor in this family with one B-box motif was cloned from B. rapa, acted as a circadian clock protein, showing expression changes during the circadian period. Additional experiments using GST pull-down and yeast two-hybrid assays indicated that BrBBX32 interacts with BrAGL24 and does not interact with BrSOC1, while BrAGL24 does interact with BrSOC1. To investigate the domains involved in these protein-protein interactions, we tested three regions of BrBBX32. Only the N-terminus interacted with BrAGL24, indicating that the B-box domain may be the key region for protein interaction. Based on these data, we propose that BrBBX32 may act in the circadian clock pathway and relate to the mechanism of flowering time regulation by binding to BrAGL24 through the B-box domain. This study will provide valuable information for unraveling the molecular regulatory mechanisms of BrBBX32 in flowering time of B. rapa.

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A genetic characterization of Korean waxy maize (Zea mays L.) landraces having flowering time variation by RNA sequencing

Scientific Reports ◽

10.1038/s41598-019-56645-y ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Gibum Yi ◽

Hosub Shin ◽

Seung Hwa Yu ◽

Jeong Eun Park ◽

Taegu Kang ◽

...

Keyword(s):

Flowering Time ◽

Time Variation ◽

Expression Profiles ◽

Genetic Relationships ◽

Gene Expression Profiles ◽

Genetic Characteristics ◽

Maize Germplasm ◽

Nucleotide Sequence Level ◽

Gene Profiles ◽

Breeding Resources

AbstractMaize is the second-most produced crop in the Korean peninsula and has been continuously cultivated since the middle of the 16th century, when it was originally introduced from China. Even with this extensive cultivation history, the diversity and properties of Korean landraces have not been investigated at the nucleotide sequence level. We collected 12 landraces with various flowering times and performed RNA-seq in the early vegetative stage. The transcriptomes of 12 Korean landraces have been analyzed for their genetic variations in coding sequence and genetic relationships to other maize germplasm. The Korean landraces showed specific genetic characteristics and were closely related to a Chinese inbred line. Flowering-time related gene profiles pointed to multiple causes for the variation of flowering time within Korean landraces; the profiles revealed significant positive and negative correlations among genes, allowing us to infer possible mechanisms for flowering time variation in maize. Our results demonstrate the value of transcriptome-based genetic and gene expression profiles for information on possible breeding resources, which is particularly needed in Korean waxy landraces.

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