Abstract:
BACKGROUND:Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) provide a promising tool for the detection and fine mapping of quantitative trait loci (QTL) underlying complex agronomic traits. In this study we explored the genetic basis of variation for the traits heading date, plant height, thousand grain weight, starch content and crude protein content in a diverse collection of 224 spring barleys of worldwide origin. The whole panel was genotyped with a customized oligonucleotide pool assay containing 1536 SNPs using Illumina's GoldenGate technology resulting in 957 successful SNPs covering all chromosomes. The morphological trait "row type" (two-rowed spike vs. six-rowed spike) was used to confirm the high level of selectivity and sensitivity of the approach. This study describes the detection of QTL for the above mentioned agronomic traits by GWAS. RESULTS:Population structure in the panel was investigated by various methods and six subgroups that are mainly based on their spike morphology and region of origin. We explored the patterns of linkage disequilibrium (LD) among the whole panel for all seven barley chromosomes. Average LD was observed to decay below a critical level (r2-value 0.2) within a map distance of 5-10 cM. Phenotypic variation within the panel was reasonably large for all the traits. The heritabilities calculated for each trait over multi-environment experiments ranged between 0.90-0.95. Different statistical models were tested to control spurious LD caused by population structure and to calculate the P-value of marker-trait associations. Using a mixed linear model with kinship for controlling spurious LD effects, we found a total of 171 significant marker trait associations, which delineate into 107 QTL regions. Across all traits these can be grouped into 57 novel QTL and 50 QTL that are congruent with previously mapped QTL positions. CONCLUSIONS:Our results demonstrate that the described diverse barley panel can be efficiently used for GWAS of various quantitative traits, provided that population structure is appropriately taken into account. The observed significant marker trait associations provide a refined insight into the genetic architecture of important agronomic traits in barley. However, individual QTL account only for a small portion of phenotypic variation, which may be due to insufficient marker coverage and/or the elimination of rare alleles prior to analysis. The fact that the combined SNP effects fall short of explaining the complete phenotypic variance may support the hypothesis that the expression of a quantitative trait is caused by a large number of very small effects that escape detection. Notwithstanding these limitations, the integration of GWAS with biparental linkage mapping and an ever increasing body of genomic sequence information will facilitate the systematic isolation of agronomically important genes and subsequent analysis of their allelic diversity.
journal_name
BMC Plant Bioljournal_title
BMC plant biologyauthors
Pasam RK,Sharma R,Malosetti M,van Eeuwijk FA,Haseneyer G,Kilian B,Graner Adoi
10.1186/1471-2229-12-16subject
Has Abstractpub_date
2012-01-27 00:00:00pages
16issn
1471-2229pii
1471-2229-12-16journal_volume
12pub_type
杂志文章abstract:BACKGROUND:Papaya (Carica papaya L.) is a commercially important crop that produces climacteric fruits with a soft and sweet pulp that contain a wide range of health promoting phytochemicals. Despite its importance, little is known about transcriptional modifications during papaya fruit ripening and their control. In t...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-12-242
更新日期:2012-12-21 00:00:00
abstract:BACKGROUND:Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F2 population by using specific length amp...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2172-5
更新日期:2019-12-27 00:00:00
abstract:BACKGROUND:Coccinia grandis is a dioecious species of Cucurbitaceae having heteromorphic sex chromosomes. The chromosome constitution of male and female plants is 22 + XY and 22 + XX respectively. Y chromosome of male sex is conspicuously large and plays a decisive role in determining maleness. Sex modification has bee...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-014-0325-0
更新日期:2014-11-28 00:00:00
abstract:BACKGROUND:The cellulose synthase superfamily has been classified into nine cellulose synthase-like (Csl) families and one cellulose synthase (CesA) family. The Csl families have been proposed to be involved in the synthesis of the backbones of hemicelluloses of plant cell walls. With 17 plant and algal genomes fully s...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-9-99
更新日期:2009-07-31 00:00:00
abstract:BACKGROUND:Phosphoenolpyruvate carboxylase (PEPC) is a critical enzyme catalyzing the β-carboxylation of phosphoenolpyruvate (PEP) to oxaloacetate, a tricarboxylic acid (TCA) cycle intermediate. PEPC typically exists as a Class-1 PEPC homotetramer composed of plant-type PEPC (PTPC) polypeptides, and two of the subunits...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-200
更新日期:2010-09-14 00:00:00
abstract:BACKGROUND:Leaves are determinate organs; hence, precise control of cell proliferation and post-mitotic cell expansion is essential for their growth. A defect in cell proliferation often triggers enhanced post-mitotic cell expansion in leaves. This phenomenon is referred to as 'compensation'. Several lines of evidence ...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-13-143
更新日期:2013-09-28 00:00:00
abstract:BACKGROUND:Hydroxyproline rich glycoproteins (HRGPs) are implicated to have a role in many aspects of plant growth and development but there is limited knowledge about their localization and function during somatic embryogenesis of higher plants. In this study, the localization and function of hydroxyproline rich glyco...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-11-38
更新日期:2011-02-24 00:00:00
abstract:BACKGROUND:The function of 4-coumarate-CoA ligases (4CL) under abiotic stresses has been studied in plants, however, limited is known about the 4CL genes in cotton (G. hirsutum L.) and their roles in response to drought stress. RESULTS:We performed genome-wide identification of the 4CL genes in G. hirsutum and investi...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-2329-2
更新日期:2020-03-23 00:00:00
abstract:BACKGROUND:Bacterial blight of rice, caused by Xanthomonas oryzae pv. oryzae (Xoo), is a devastating rice disease in Southeast Asia and West Africa. OsSWEET14, encoding a sugar transporter, is known to be a major susceptible gene of bacterial blight targeted by four different transcription activator-like (TAL) effector...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02524-y
更新日期:2020-07-03 00:00:00
abstract:BACKGROUND:MicroRNAs play important roles in the adaptive responses of plants to nutrient deficiencies. Most research, however, has focused on nitrogen (N), phosphorus (P), sulfur (S), copper (Cu) and iron (Fe) deficiencies, limited data are available on the differential expression of miRNAs and their target genes in r...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-015-0642-y
更新日期:2015-11-04 00:00:00
abstract:BACKGROUND:Species in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug ...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-017-1115-2
更新日期:2017-10-30 00:00:00
abstract:BACKGROUND:Under natural conditions, soil nutrients are heterogeneously distributed, and plants have developed adaptation strategies to efficiently forage patchily distributed nutrient. Most previous studies examined either patch strength or patch size separately and focused mainly on root morphological plasticity (inc...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02738-0
更新日期:2020-12-07 00:00:00
abstract:BACKGROUND:Overuse of nitrogen fertilizers is often a major practice to ensure sufficient nitrogen demand of high-yielding rice, leading to persistent NH4+ excess in the plant. However, this excessive portion of nitrogen nutrient does not correspond to further increase in grain yields. For finding out the main constrai...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02363-x
更新日期:2020-04-07 00:00:00
abstract:BACKGROUND:Somatic embryogenesis (SE) is an asexual propagation pathway requiring a somatic-to-embryonic transition of differentiated somatic cells toward embryogenic cells capable of producing embryos in a process resembling zygotic embryogenesis. In chicory, genetic variability with respect to the formation of somati...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-7-27
更新日期:2007-06-06 00:00:00
abstract:BACKGROUND:Nectar is a major floral attractant and reward for insects that ensures pollination. Liriodendron, a genus of the Magnoliaceae family, includes only two relict species, L. chinense and L. tulipifera, which are considered "basal angiosperms" according to plant evolutionary history. The flowers of Liriodendron...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-019-2140-0
更新日期:2019-12-02 00:00:00
abstract:BACKGROUND:Arabidopsis ovules comprise four morphologically distinct parts: the nucellus, which contains the embryo sac, two integuments that become the seed coat, and the funiculus that anchors the ovule within the carpel. Analysis of developmental mutants has shown that ovule morphogenesis relies on tightly regulated...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-9-29
更新日期:2009-03-16 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. There is growing evidence that they are associated with development; but their expression and regulation during fruit ripening in the model plant tomato (Solanum lycopersicum) has yet to be described. RE...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1300-y
更新日期:2018-05-04 00:00:00
abstract:BACKGROUND:Lycoris species have great ornamental and medicinal values; however, their low regeneration efficiency seriously restricts their commercial production. Understanding the mechanism of bulblet propagation in this genus, which has remained underexplored to date, could provide a theoretical basis for improving t...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02394-4
更新日期:2020-04-25 00:00:00
abstract:BACKGROUND:Most of the natural variation in flowering time in Arabidopsis thaliana can be attributed to allelic variation at the gene FRIGIDA (FRI, AT4G00650), which activates expression of the floral repressor FLOWERING LOCUS C (FLC, AT5G10140). Usually, late-flowering accessions carry functional FRI alleles (FRI-wt),...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-014-0218-2
更新日期:2014-08-13 00:00:00
abstract:BACKGROUND:The translocator protein 18 kDa (TSPO), previously known as the peripheral-type benzodiazepine receptor (PBR), is important for many cellular functions in mammals and bacteria, such as steroid biosynthesis, cellular respiration, cell proliferation, apoptosis, immunomodulation, transport of porphyrins and ani...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-11-108
更新日期:2011-06-20 00:00:00
abstract:BACKGROUND:Dehydrins play positive roles in regulating plant abiotic stress responses. The objective of this study was to characterize two dehydrin genes, CdDHN4-L and CdDHN4-S, generated by alternative splicing of CdDHN4 in bermudagrass. RESULTS:Overexpression of CdDHN4-L with φ-segment and CdDHN4-S lacking of φ-segm...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-018-1511-2
更新日期:2018-11-26 00:00:00
abstract:BACKGROUND:While floral symmetry has traditionally been assessed qualitatively, recent advances in geometric morphometrics have opened up new avenues to specifically quantify flower shape and size using robust multivariate statistical methods. In this study, we examine, for the first time, the ability of geometric morp...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-017-1152-x
更新日期:2017-11-17 00:00:00
abstract:BACKGROUND:Currently, Tectona grandis is one of the most valuable trees in the world and no transcript dataset related to secondary xylem is available. Considering how important the secondary xylem and sapwood transition from young to mature trees is, little is known about the expression differences between those succe...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-015-0599-x
更新日期:2015-09-15 00:00:00
abstract:BACKGROUND:Powdery mildew of barley is a wind-borne and obligate biotrophic pathogen, which ranks among the most widespread barley pathogens worldwide. However, purposeful research towards studying the structure of the barley powdery mildew populations, of their virulence and of effectiveness of certain resistance gene...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-017-1130-3
更新日期:2017-11-14 00:00:00
abstract:BACKGROUND:Symptoms of grapevine leafroll disease (GLRD) in red-fruited wine grape (Vitis vinifera L.) cultivars consist of green veins and red and reddish-purple discoloration of inter-veinal areas of leaves. The reddish-purple color of symptomatic leaves may be due to the accumulation of anthocyanins and could reflec...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-187
更新日期:2010-08-23 00:00:00
abstract:BACKGROUND:Dwarf bunt, which is caused by Tilletia controversa Kühn, is a soilborne and seedborne disease that occurs worldwide and can lead to 70% or even total losses of wheat crops. However, very little information is available about the histological changes that occur in dwarf bunt-resistant and dwarf bunt-suscepti...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-020-02819-0
更新日期:2021-01-18 00:00:00
abstract:BACKGROUND:Mitochondria are dynamic organelles that move along actin filaments, and serve as calcium stores in plant cells. The positioning and dynamics of mitochondria depend on membrane-cytoskeleton interactions, but it is not clear whether microfilament cytoskeleton has a direct effect on mitochondrial function and ...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-10-53
更新日期:2010-03-24 00:00:00
abstract:BACKGROUND:The RAD21 cohesin plays, besides its well-recognised role in chromatid cohesion, a role in DNA double strand break (dsb) repair. In Arabidopsis there are three RAD21 paralog genes (AtRAD21.1, AtRAD21.2 and AtRAD21.3), yet only AtRAD21.1 has been shown to be required for DNA dsb damage repair. Further investi...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/s12870-014-0353-9
更新日期:2014-12-16 00:00:00
abstract:BACKGROUND:Canola (Brassica napus L.) is one of the most important oil-producing crops in China and worldwide. The yield and quality of canola is frequently threatened by environmental stresses including drought, cold and high salinity. Calcium is a ubiquitous intracellular secondary messenger in plants. Calcineurin B-...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-14-8
更新日期:2014-01-07 00:00:00
abstract:BACKGROUND:Retrotransposons are heterogeneous sequences, widespread in eukaryotic genomes, which refer to the so-called mobile DNA. They resemble retroviruses, both in their structure and for their ability to transpose within the host genome, of which they make up a considerable portion. Copia- and Gypsy-like retrotran...
journal_title:BMC plant biology
pub_type: 杂志文章
doi:10.1186/1471-2229-9-150
更新日期:2009-12-23 00:00:00