Flt-2L, a locus in barley controlling flowering time, spike density, and plant height

Within the cereal grasses, variation in inflorescence architecture results in a conspicuous morphological diversity that in crop species influences the yield of cereal grains. Although significant progress has been made in identifying some of the genes underlying this variation in maize and rice, in the temperate cereals, a group that includes wheat, barley, and rye, only the dosagedependent and highly pleiotropic Q locus in hexaploid wheat has been molecularly characterized. Here we show that the characteristic variation in the density of grains along the inflorescence, or spike, of modern cultivated barley (Hordeum vulgare) is largely the consequence of a perturbed interaction between microRNA172 and its corresponding binding site in the mRNA of an APELATA2 (AP2)-like transcription factor, HvAP2. We used genome-wide association and biparental mapping to identify HvAP2. By comparing inflorescence development and HvAP2 transcript abundance in an extreme dense-spike mutant and its nearly isogenic WT line, we show that HvAP2 turnover driven by microRNA 172 regulates the length of a critical developmental window that is required for elongation of the inflorescence internodes. Our data indicate that this heterochronic change, an altered timing of developmental events caused by specific temporal variation in the efficiency of HvAP2 turnover, leads to the striking differences in the size and shape of the barley spike.genome wide association scan | heterochrony T he cereal grasses are the world's most economically, sociologically, and ecologically important crops (1). Within and between species, variation in inflorescence architecture results in striking and characteristic morphological diversity. Dissecting the mechanisms and processes underpinning this diversity is central to understanding both its origin and evolution and how it can be harnessed for knowledge-based crop improvement. In maize and rice, a considerable body of work has begun to dissect the genes and gene networks controlling aspects of inflorescence development (e.g., refs. 2-5). However, within the Triticeae cereals, a group that includes some of the world's most important human foods, only Q, a highly pleiotropic gene that influences a broad range of phenotypic characters including inflorescence compactness, fragility, and free-threshing (6), and genes that determine the development of an extra floret on the lemma (7), additional glumes (8), the number of grains on the inflorescence (9), and floret fertility (10) have been molecularly characterized.Barley is a diploid inbreeding crop species and a model for other, genetically more complex temperate cereal species such as durum and bread wheats and rye. The barley inflorescence forms a terminal spike that bears reproductive units called "spikelets." Three spikelets initiate at each alternating node of the spike's central stem or rachis. Each spikelet forms a single floret that can develop into a kernel of grain. Several loci have been shown to affect spike density in barley (11), including dense spike...

show abstract

“…1D). This position is consistent with that of previously identified QTL for the orthologous phenotype "rachis internode length" (15,16).…”

Section: Resultssupporting

confidence: 79%

Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence

Houston

McKim

Comadran

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

119

108

View full text Add to dashboard Cite

show abstract

“…This marker is significantly associated with frost tolerance with both ‘Intro’ and ‘Tokak’ possessing the more tolerant allele. The significant association found with SNP 11_20366 on the long arm of chromosome 2H at 128 cM is in the same region as the FLT-2L flowering locus [35], which has also been reported to be closely linked to a QTL controlling frost induced sterility at the reproductive stage [17,18], although this association was only significant in the EIGENSTRAT analysis. At this locus, ‘Tokak’ carries the more tolerant allele and ‘Intro’ the more susceptible one.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)

et al. 2013

View full text Add to dashboard Cite

BackgroundFrost tolerance is a key trait with economic and agronomic importance in barley because it is a major component of winter hardiness, and therefore limits the geographical distribution of the crop and the effective transfer of quality traits between spring and winter crop types. Three main frost tolerance QTL (Fr-H1, Fr-H2 and Fr-H3) have been identified from bi-parental genetic mapping but it can be argued that those mapping populations only capture a portion of the genetic diversity of the species. A genetically broad dataset consisting of 184 genotypes, representative of the barley gene pool cultivated in the Mediterranean basin over an extended time period, was genotyped with 1536 SNP markers. Frost tolerance phenotype scores were collected from two trial sites, Foradada (Spain) and Fiorenzuola (Italy) and combined with the genotypic data in genome wide association analyses (GWAS) using Eigenstrat and kinship approaches to account for population structure.ResultsGWAS analyses identified twelve and seven positive SNP associations at Foradada and Fiorenzuola, respectively, using Eigenstrat and six and four, respectively, using kinship. Linkage disequilibrium analyses of the significant SNP associations showed they are genetically independent. In the kinship analysis, two of the significant SNP associations were tightly linked to the Fr-H2 and HvBmy loci on chromosomes 5H and 4HL, respectively. The other significant kinship associations were located in genomic regions that have not previously been associated with cold stress.ConclusionsHaplotype analysis revealed that most of the significant SNP loci are fixed in the winter or facultative types, while they are freely segregating within the un-adapted spring barley genepool. Although there is a major interest in detecting new variation to improve frost tolerance of available winter and facultative types, from a GWAS perspective, working within the un-adapted spring germplasm pool is an attractive alternative strategy which would minimize statistical issues, simplify the interpretation of the data and identify phenology independent genetic determinants of frost tolerance.

show abstract

“…Additionally, genes involved in flowering time also play a role in PH regulation, such as DTH8 and Ghd7 in rice (Xue et al, 2008; Wei et al, 2010), and Flt-2L in wheat (Chen et al, 2009). In rapeseed, Mei et al (2009) found an overlap between a flowering time locus and PH QTLs.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed (Brassica napus L.)

et al. 2017

View full text Add to dashboard Cite

Plant architecture is crucial for rapeseed yield and is determined by plant height (PH), branch initiation height (BIH), branch number (BN) and leaf and inflorescence morphology. In this study, we measured three major factors (PH, BIH, and BN) in a panel of 333 rapeseed accessions across 4 years. A genome-wide association study (GWAS) was performed via Q + K model and the panel was genotyped using the 60 k Brassica Infinium SNP array. We identified seven loci for PH, four for BIH, and five for BN. Subsequently, by determining linkage disequilibrium (LD) decay associated with 38 significant SNPs, we gained 31, 15, and 17 candidate genes for these traits, respectively. We also showed that PH is significantly correlated with BIH, while no other correlation was revealed. Notably, a GA signaling gene (BnRGA) and a flowering gene (BnFT) located on chromosome A02 were identified as the most likely candidate genes associated with PH regulation. Furthermore, a meristem initiation gene (BnLOF2) and a NAC domain transcriptional factor (BnCUC3) that may be associated with BN were identified on the chromosome A07. This study reveals novel insight into the genetic control of plant architecture and may facilitate marker-based breeding for rapeseed.

show abstract

Flt-2L, a locus in barley controlling flowering time, spike density, and plant height

Cited by 45 publications

References 55 publications

Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence

Variation in the interaction between alleles of HvAPETALA2 and microRNA172 determines the density of grains on the barley inflorescence

Genome-wide association mapping of frost tolerance in barley (Hordeum vulgare L.)

Genome-Wide Association Study Reveals Candidate Genes for Control of Plant Height, Branch Initiation Height and Branch Number in Rapeseed (Brassica napus L.)

Contact Info

Product

Resources

About