Modelling the genetic architecture of flowering time control in barley through nested association mapping

Abstract Intermediate wheatgrass (Thinopyrum intermedium) is an outcrossing, cool season grass species currently undergoing direct domestication as a perennial grain crop. Though many traits are selection targets, understanding the genetic architecture of those important for local adaptation may accelerate the domestication process. Nested association mapping (NAM) has proven useful in dissecting the genetic control of agronomic traits many crop species, but its utility in primarily outcrossing, perennial species has yet to be demonstrated. Here we introduce an intermediate wheatgrass NAM developed by crossing ten phenotypically divergent donor parents to an adapted common parent in a reciprocal manner, yielding 1,168 F1 progeny from 10 families. Using genotyping by sequencing, we identified 8,003 SNP markers and developed a population-specific consensus genetic map with 3,144 markers across 21 linkage groups. Using both genomewide association mapping and linkage mapping combined across and within families, we characterize the genetic control of flowering time. In the analysis of two measures of maturity across four separate environments, we detected as many as 75 significant QTL, many of which correspond to the same regions in both analysis methods across 11 chromosomes. The results demonstrate a complex genetic control that is variable across years, locations, traits, and within families. The methods were effective at detecting previously identified QTL, as well as new QTL that align closely to the well-characterized flowering time orthologs from barley, including Ppd-H1 and Constans. Our results demonstrate the utility of the NAM for understanding the genetic control of flowering time and its potential for application to other traits of interest.

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Recent Advances in Flowering Time Control

10.3389/978-2-88945-115-9 ◽

2017 ◽

Keyword(s):

Flowering Time ◽

Time Control ◽

Recent Advances ◽

Flowering Time Control

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New Nucleotide Polymorphisms in the BTC1 gene of Sugar Beet

Biotekhnologiya ◽

10.21519/0234-2758-2020-36-6-49-54 ◽

2020 ◽

Vol 36 (6) ◽

pp. 49-54

Author(s):

A.A. Nalbandyan ◽

T.P. Fedulova ◽

I.V. Cherepukhina ◽

T.I. Kryukova ◽

N.R. Mikheeva ◽

...

Keyword(s):

Sugar Beet ◽

Flowering Time ◽

Molecular Genetic ◽

Bioinformatic Analysis ◽

Early Flowering ◽

Nucleotide Polymorphisms ◽

Nucleotide Substitutions ◽

Time Control ◽

Flowering Time Control ◽

Exon 10

The flowering time control gene of various sugar beet plants has been studied. The BTC1 gene is a regulator for the suppressor (flowering time 1) and inducer (flowering time 2) genes of this physiological process. The F9/R9 primer pair was used for polymerase chain reaction; these primers are specific to the BTC1 gene region containing exon 9, as well as intron and exon 10. For the first time, nucleotide substitutions in exon 10 of BTC1 gene were identified in bolting sensitive samples (HF1 and BF1), which led to a change in the amino acid composition of the coded polypeptide chain. Based on the results of bioinformatic analysis, it can be assumed that certain nucleotide polymorphisms in the BTC1 gene may determine with a high probability the predisposition of sugar beet genotypes to early flowering. The use of the Geneious Prime tool for the analysis of the BTC1 gene sequences may allow the culling of genotypes prone to early flowering at early stages of selection. sugar beet, flowering gene, BTC1, genetic polymorphism, PCR, molecular genetic markers, selection

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Message ends: RNA 3′ processing and flowering time control

Journal of Experimental Botany ◽

10.1093/jxb/ert439 ◽

2013 ◽

Vol 65 (2) ◽

pp. 353-363 ◽

Cited By ~ 14

Author(s):

Katarzyna Rataj ◽

Gordon G. Simpson

Keyword(s):

Flowering Time ◽

Time Control ◽

Flowering Time Control

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Repeated rearrangement of the GSL‐AOP locus contributed to spatio‐temporal variation in defense chemistry in Arabidopsis

10.21203/rs.3.rs-108131/v1 ◽

2020 ◽

Author(s):

Konrad Weber ◽

Lucasz Krych ◽

Meike Burow

Keyword(s):

Flowering Time ◽

Regulatory Networks ◽

Structural Diversity ◽

Sequence Information ◽

Sequencing Data ◽

Defense Compounds ◽

Caucasus Region ◽

Time Control ◽

Spatio Temporal ◽

Flowering Time Control

Abstract Plants coordinate metabolic and developmental processes with the help of genetically variable, interconnected regulatory networks. The GSL-AOP locus in Arabidopsis thaliana encodes enzymes involved in the biosynthesis of glucosinolate defense compounds and has been attributed regulatory functions e.g. in flowering time control. To correlate genetic and phenotypic variation linked to GSL-AOP, we conducted a phylogenetic analysis across 1135 accessions and found that the available short-read sequencing data does not fully resolve the structural diversity in the locus. We analyzed a selection of 74 accessions for glucosinolate profiles and flowering time under different conditions and acquired long-read sequence information for glucosinolate and flowering time loci. Especially in the Caucasus region, structural variation in GSL-AOP was associated with conditional, tissue-specific glucosinolate profiles. Variation in FLC among the Caucasian accessions correlated with variation in the flowering time response to vernalization, suggesting that local adaptation has shaped defense and development in an orchestrated manner.

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Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat

The Plant Genome ◽

10.1002/tpg2.20051 ◽

2020 ◽

Vol 13 (3) ◽

Author(s):

Ahmad H. Sallam ◽

Fazal Manan ◽

Prabin Bajgain ◽

Matthew Martin ◽

Tamas Szinyei ◽

...

Keyword(s):

Association Mapping ◽

Spring Wheat ◽

Genetic Architecture ◽

Mapping Population ◽

Quality Traits ◽

Nested Association Mapping ◽

Nested Association Mapping Population ◽

Association Mapping Population

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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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Flowering time control in rice by introducing Arabidopsis clock-associated PSEUDO-RESPONSE REGULATOR 5

Bioscience Biotechnology and Biochemistry ◽

10.1080/09168451.2020.1719822 ◽

2020 ◽

Vol 84 (5) ◽

pp. 970-979 ◽

Cited By ~ 2

Author(s):

Norihito Nakamichi ◽

Toru Kudo ◽

Nobue Makita ◽

Takatoshi Kiba ◽

Toshinori Kinoshita ◽

...

Keyword(s):

Flowering Time ◽

Response Regulator ◽

Time Control ◽

Pseudo Response Regulator ◽

Flowering Time Control

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Flowering time control: gene network modelling and the link to quantitative genetics

Australian Journal of Agricultural Research ◽

10.1071/ar05155 ◽

2005 ◽

Vol 56 (9) ◽

pp. 919 ◽

Cited By ~ 40

Author(s):

Stephen M. Welch ◽

Zhanshan Dong ◽

Judith L. Roe ◽

Sanjoy Das

Keyword(s):

Flowering Time ◽

Quantitative Genetics ◽

Model Development ◽

Genetic Network ◽

Ideal Theory ◽

Emergent Properties ◽

Network Modelling ◽

Crop Models ◽

Time Control ◽

Flowering Time Control

Flowering is a key stage in plant development that initiates grain production and is vulnerable to stress. The genes controlling flowering time in the model plant Arabidopsis thaliana are reviewed. Interactions between these genes have been described previously by qualitative network diagrams. We mathematically relate environmentally dependent transcription, RNA processing, translation, and protein–protein interaction rates to resultant phenotypes. We have developed models (reported elsewhere) based on these concepts that simulate flowering times for novel A. thaliana genotype–environment combinations. Here we draw 12 contrasts between genetic network (GN) models of this type and quantitative genetics (QG), showing that both have equal contributions to make to an ideal theory. Physiological dominance and additivity are examined as emergent properties in the context of feed-forwards networks, an instance of which is the signal-integration portion of the A. thaliana flowering time network. Additivity is seen to be a complex, multi-gene property with contributions from mass balance in transcript production, the feed-forwards structure itself, and downstream promoter reaction thermodynamics. Higher level emergent properties are exemplified by critical short daylength (CSDL), which we relate to gene expression dynamics in rice (Oryza sativa). Next to be discussed are synergies between QG and GN relating to the quantitative trait locus (QTL) mapping of model coefficients. This suggests a new verification test useful in GN model development and in identifying needed updates to existing crop models. Finally, the utility of simple models is evinced by 80 years of QG theory and mathematical ecology.

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