Molecular Characterization of Barley 3H Semi-Dwarf Genes

The barley chromosome 3H accommodates many semi-dwarfing genes. To characterize these genes, the two-rowed semi-dwarf Chinese barley landrace ‘TX9425’ was crossed with the Australian barley variety ‘Franklin’ to generate a doubled haploid (DH) population, and major QTLs controlling plant height have been identified in our previous study. The major QTL derived from ‘TX9425’ was targeted to investigate the allelism of the semi-dwarf gene uzu in barley. Twelve sets of near-isogenic lines and a large NILF₂ fine mapping population segregating only for the dwarfing gene from ‘TX9425’ were developed. The semi-dwarfing gene in ‘TX9425’ was located within a 2.8 cM region close to the centromere on chromosome 3H by fine mapping. Molecular cloning and sequence analyses showed that the ‘TX9425’-derived allele contained a single nucleotide substitution from A to G at position 2612 of the HvBRI1 gene. This was apparently the same mutation as that reported in six-rowed uzu barley. Markers co-segregating with the QTL were developed from the sequence of the HvBRI1 gene and were validated in the ‘TX9425’/‘Franklin’ DH population. The other major dwarfing QTL derived from the Franklin variety was distally located on chromosome 3HL and co-segregated with the sdw1 diagnostic marker hv20ox2. A third dwarfing gene, expressed only in winter-sown trials, was identified and located on chromosome 3HS. The effects and interactions of these dwarfing genes under different growing conditions are discussed. These results improve our understanding of the genetic mechanisms controlling semi-dwarf stature in barley and provide diagnostic markers for the selection of semi-dwarfness in barley breeding programs.     

Sugar composition of the pectic polysaccharides of charophytes,the closest algal relatives of land-plants: presence of 3-O-methyl-d-galactose residues

Background and Aims During evolution, plants have acquired and/or lost diverse sugar residues as cell-wall constituents. Of particular interest are primordial cell-wall features that existed, and in some cases abruptly changed, during the momentous step whereby land-plants arose from charophytic algal ancestors.Methods Polysaccharides were extracted from four charophyte orders [Chlorokybales (Chlorokybus atmophyticus), Klebsormidiales (Klebsormidium fluitans, K. subtile), Charales (Chara vulgaris, Nitella flexilis), Coleochaetales (Coleochaete scutata)] and an early-diverging land-plant (Anthoceros agrestis). ‘Pectins’ and ‘hemicelluloses’, operationally defined as extractable in oxalate (100 °C) and 6 m NaOH (37 °C), respectively, were acid- or Driselase-hydrolysed, and the monosaccharides analysed chromatographically. One unusual monosaccharide, ‘U’, was characterized by ¹H/¹³C-nuclear magnetic resonance spectroscopy and also enzymically.Key Results ‘U’ was identified as 3-O-methyl-d-galactose (3-MeGal). All pectins, except in Klebsormidium, contained acid- and Driselase-releasable galacturonate, suggesting homogalacturonan. All pectins, without exception, released rhamnose and galactose on acid hydrolysis; however, only in ‘higher’ charophytes (Charales, Coleochaetales) and Anthoceros were these sugars also efficiently released by Driselase, suggesting rhamnogalacturonan-I. Pectins of ‘higher’ charophytes, especially Chara, contained little arabinose, instead possessing 3-MeGal. Anthoceros hemicelluloses were rich in glucose, xylose, galactose and arabinose (suggesting xyloglucan and arabinoxylan), none of which was consistently present in charophyte hemicelluloses.Conclusions Homogalacturonan is an ancient streptophyte feature, albeit secondarily lost in Klebsormidium. When conquering the land, the first embryophytes already possessed rhamnogalacturonan-I. In contrast, charophyte and land-plant hemicelluloses differ substantially, indicating major changes during terrestrialization. The presence of 3-MeGal in charophytes and lycophytes but not in the ‘intervening’ bryophytes confirms that cell-wall chemistry changed drastically between major phylogenetic grades.     

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

Clinical mastitis (CM) is an inflammatory disease occurring in the mammary glands of lactating cows. CM is under genetic control, and a prominent CM resistance QTL located on chromosome 6 was reported in various dairy cattle breeds. Nevertheless, the biological mechanism underpinning this QTL has been lacking. Herein, we mapped, fine-mapped, and discovered the putative causal variant underlying this CM resistance QTL in the Dutch dairy cattle population. We identified a ~12 kb multi-allelic copy number variant (CNV), that is in perfect linkage disequilibrium with a lead SNP, as a promising candidate variant. By implementing a fine-mapping and through expression QTL mapping, we showed that the group-specific component gene (GC), a gene encoding a vitamin D binding protein, is an excellent candidate causal gene for the QTL. The multiplicated alleles are associated with increased GC expression and low CM resistance. Ample evidence from functional genomics data supports the presence of an enhancer within this CNV, which would exert cis-regulatory effect on GC. We observed that strong positive selection swept the region near the CNV, and haplotypes associated with the multiplicated allele were strongly selected for. Moreover, the multiplicated allele showed pleiotropic effects for increased milk yield and reduced fertility, hinting that a shared underlying biology for these effects may revolve around the vitamin D pathway. These findings together suggest a putative causal variant of a CM resistance QTL, where a cis-regulatory element located within a CNV can alter gene expression and affect multiple economically important traits.     

Precisely mapping a major gene conferring resistance to Hessian fly in bread wheat using genotyping-by-sequencing

Background

One of the reasons hard red winter wheat cultivar ‘Duster’ (PI 644016) is widely grown in the southern Great Plains is that it confers a consistently high level of resistance to biotype GP of Hessian fly (Hf). However, little is known about the genetic mechanism underlying Hf resistance in Duster. This study aimed to unravel complex structures of the Hf region on chromosome 1AS in wheat by using genotyping-by-sequencing (GBS) markers and single nucleotide polymorphism (SNP) markers.

Results

Doubled haploid (DH) lines generated from a cross between two winter wheat cultivars, ‘Duster’ and ‘Billings’ , were used to identify genes in Duster responsible for effective and consistent resistance to Hf. Segregation in reaction of the 282 DH lines to Hf biotype GP fit a one-gene model. The DH population was genotyped using 2,358 markers developed using the GBS approach. A major QTL, explaining 88% of the total phenotypic variation, was mapped to a chromosome region that spanned 178 cM and contained 205 GBS markers plus 1 SSR marker and 1 gene marker, with 0.86 cM per marker in genetic distance. The analyses of GBS marker sequences and further mapping of SSR and gene markers enabled location of the QTL-containing linkage group on the short arm of chromosome 1A. Comparative mapping of the common markers for the gene for QHf.osu-1A^d in Duster and the Hf-resistance gene for QHf.osu-1A⁷⁴ in cultivar ‘2174’ showed that the two Hf resistance genes are located on the same chromosome arm 1AS, only 11.2 cM apart in genetic distance. The gene at QHf.osu-1A^d in Duster has been delimited within a 2.7 cM region.

Conclusion

Two distinct resistance genes exist on the short arm of chromosome 1A as found in the two hard red winter cultivars, 2174 and Duster. Whereas the Hf resistance gene in 2174 is likely allelic to one or more of the previously mapped resistance genes (H9, H10, H11, H16, or H17) in wheat, the gene in Duster is novel and confers a more consistent phenotype than 2174 in response to biotype GP infestation in controlled-environment assays.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1297-7) contains supplementary material, which is available to authorized users.     

Genetic Features of the Spontaneous Self-Compatible Mutant, ‘Jin Zhui’ (Pyrus bretschneideri Rehd.)

‘Jin Zhui’ is a spontaneous self-compatible mutant of ‘Ya Li’ (Pyrus bretschneideri Rehd. S₂₁S₃₄), the latter displaying a typical S-RNase-based gametophytic self-incompatibility (GSI). The pollen-part mutation (PPM) of ‘Jin Zhui’ might be due to a natural mutation in the pollen-S gene (S₃₄ haplotype). However, the molecular mechanisms behind these phenotypic changes are still unclear. In this study, we identified five SLF (S-Locus F-box) genes in ‘Ya Li’, while no nucleotide differences were found in the SLF genes of ‘Jin Zhui’. Further genetic analysis by S-RNase PCR-typing of selfed progeny of ‘Jin Zhui’ and ‘Ya Li’ × ‘Jin Zhui’ progeny showed three progeny classes (S₂₁S₂₁, S₂₁S₃₄ and S₃₄S₃₄) as opposed to the two classes reported previously (S₂₁S₃₄ and S₃₄S₃₄), indicating that the pollen gametes of ‘Jin Zhui’, bearing either the S₂₁- or S₃₄-haplotype, were able to overcome self-incompatibility (SI) barriers. Moreover, no evidence of pollen-S duplication was found. These findings support the hypothesis that loss of function of S-locus unlinked PPM expressed in pollen leads to SI breakdown in ‘Jin Zhui’, rather than natural mutation in the pollen-S gene (S₃₄ haplotype). Furthermore, abnormal meiosis was observed in a number of pollen mother cells (PMCs) in ‘Jin Zhui’, but not in ‘Ya Li’. These and other interesting findings are discussed.     

Chromosome mapping in barley by means of telotrisomic analysis

Summary A total of 37 genetic markers located in chromosomes 2, 3, 4 and 5 were associated with specific arms by means of telotrisomic analysis in five telotrisomics (Triplo 2 L, 2 S, 3 S, 4 S, 5 L) of barley (Hordeum vulgare L.). The genes v, gp (= gp 2), li, gs 5, tr and msg2 showed a trisomic ratio with Triplo 2 L indicating that these genes were on the long arm of chromosome 2. A disomic ratio was obtained for genes wst 4, gs 5, and v with Triplo 2 S, confirming that these genes were on the long arm of chromosome 2(2 L). A disomic ratio was observed for genes e, f(= lg), sk, and gs6 with Triplo 2 L. Two genes, f(= lg) and gs6 showed a trisomic ratio with Triplo 2S. These results indicated that genes e, f(= lg), sk, and gs 6 are on the short arm of chromosome 2 (2S). Since only one telocentric chromosome was available for chromosome 3, 4 and 5, most of the well-mapped marker genes were tested with those telocentric chromosomes. The genes cu 2, uz, wst, als, gs 2, zb,f2, and cer-zn ³⁴⁸ showed trisomic ratio with the telocentric for chromosome 3. These genes were located on the short arm of chromosome 3 (Robertson 1971). This indicated that the telocentric chromosome is for the short arm of chromosome 3(3 S). A disomic ratio was obtained for genes yst, x _c, al, yst2, a _n, ari-a ⁶ and x _s, indicating that these genes are on the long arm of chromosome 3. Two genes, f9 and K, showed trisomic ratio with the telocentric chromosome for 4, while genes gl(= gl2), br2, yh, lg 3, lg 4 and lk 5 showed disomic ratios. This indicated that the telocentric chromosome is for the short arm of chromosome 4. Two genes, fs 2 and g, were studied with Triplo 5 L. Both showed trisomic ratio, indicating that fs 2 and g are located on Triplo 5 L. The centromere position (C) on chromosome 2, 3 and 4 was thus located as (the left side of C is the short arm and the right is the long arm): chromosome 2: f — sk — gs6 — e — C — gs5 — msg2 — wst4 — v — gp — li — tr; chromosome 3: f2 — cer-zn ³⁴⁸ — uz — gs2 — als — cu2 — wst — zb — C — yst — x _c — al — yst2 — a _n — ari-a ⁶ — x _s; chromosome 4: f9 — K — C — lg4 — lg ³ — gl2 — br2 — lk5 — yh. The centromere position on chromosome 5 was not precisely located.Contribution from the Department of Agronomy, Published with the approval of the director of the Colorado State University Experiment Station as Scientific Series Paper No. 2606. This research was supported in part by by NSF Grant GB 4482X and GB 30 493 to T. Tsuchiya and Colorado State University Experiment Station Hatch Project     

Combination Patterns of Major R Genes Determine the Level of Resistance to the M. oryzae in Rice (Oryza sativa L.)

Rice blast caused by Magnaporthe oryzae is the most devastating disease of rice and poses a serious threat to world food security. In this study, the distribution and effectiveness of 18 R genes in 277 accessions were investigated based on pathogenicity assays and molecular markers. The results showed that most of the accessions exhibited some degree of resistance (resistance frequency, RF >50%). Accordingly, most of the accessions were observed to harbor two or more R genes, and the number of R genes harbored in accessions was significantly positively correlated with RF. Some R genes were demonstrated to be specifically distributed in the genomes of rice sub-species, such as Pigm, Pi9, Pi5 and Pi1, which were only detected in indica-type accessions, and Pik and Piz, which were just harbored in japonica-type accessions. By analyzing the relationship between R genes and RF using a multiple stepwise regression model, the R genes Pid3, Pi5, Pi9, Pi54, Pigm and Pit were found to show the main effects against M. oryzae in indica-type accessions, while Pita, Pb1, Pik, Pizt and Pia were indicated to exhibit the main effects against M. oryzae in japonica-type accessions. Principal component analysis (PCA) and cluster analysis revealed that combination patterns of major R genes were the main factors determining the resistance of rice varieties to M. oryzae, such as ‘Pi9+Pi54’, ‘Pid3+Pigm’, ‘Pi5+Pid3+Pigm’, ‘Pi5+Pi54+Pid3+Pigm’, ‘Pi5+Pid3’ and ‘Pi5+Pit+Pid3’ in indica-type accessions and ‘Pik+Pib’, ‘Pik+Pita’, ‘Pik+Pb1’, ‘Pizt+Pia’ and ‘Pizt+Pita’ in japonica-type accessions, which were able to confer effective resistance against M. oryzae. The above results provide good theoretical support for the rational utilization of combinations of major R genes in developing rice cultivars with broad-spectrum resistance.     

New genes with old modus operandi. The connection between supercoiling and partitioning of DNA in Escherichia coli

The process of partitioning bacterial sister chromosomes into daughter cells seems to be distinct from chromatid segregation during eukaryotic mitosis. In Escherichia coli, partitioning starts soon after initiation of replication, when the two newly replicated oriCs move from the cell centre to quarter positions within the cell. As replication proceeds, domains of the compact, supercoiled chromosome are locally decondensed ahead of the replication fork. The nascent daughter chromosomes are recondensed and moved apart through the concerted activities of topoisomerases and the SeqA (sequestration) and MukB (chromosome condensation) proteins, all of which modulate nucleoid superhelicity. Thus, genes involved in chromosome topology, once set aside as ‘red herrings’ in the search for ‘true’ partition functions, are again recognized as being important for chromosome partitioning in E. coli.     

The DNA binding CXC domain of MSL2 is required for faithful targeting the Dosage Compensation Complex to the X chromosome

Dosage compensation in Drosophila melanogaster involves the selective targeting of the male X chromosome by the dosage compensation complex (DCC) and the coordinate, ∼2-fold activation of most genes. The principles that allow the DCC to distinguish the X chromosome from the autosomes are not understood. Targeting presumably involves DNA sequence elements whose combination or enrichment mark the X chromosome. DNA sequences that characterize ‘chromosomal entry sites’ or ‘high-affinity sites’ may serve such a function. However, to date no DNA binding domain that could interpret sequence information has been identified within the subunits of the DCC. Early genetic studies suggested that MSL1 and MSL2 serve to recognize high-affinity sites (HAS) in vivo, but a direct interaction of these DCC subunits with DNA has not been studied. We now show that recombinant MSL2, through its CXC domain, directly binds DNA with low nanomolar affinity. The DNA binding of MSL2 or of an MSL2–MSL1 complex does not discriminate between different sequences in vitro, but in a reporter gene assay in vivo, suggesting the existence of an unknown selectivity cofactor. Reporter gene assays and localization of GFP-fusion proteins confirm the important contribution of the CXC domain for DCC targeting in vivo.     

Association of polymorphisms in the toll-like receptor genes with atopic dermatitis in the Republic of Bashkortostan

Atopic dermatitis is a common chronic inflammatory skin disease and depends on the interaction between environmental factors and genetic predisposition. A considerable role in allergic disorders is played by polymorphisms of the genes of pattern recognition receptors (PRRs), which recognize conserved standard molecular structures (patterns) unique to large pathogen groups. Polymorphisms of several PRR genes, including the genes of Toll-like receptors (TLR1, TLR2, TLR4, TLR5, TLR6, TLR9, and TLR10), NOD-like receptors (NOD1 and NOD2), and a lipopolysaccharide receptor (CD14) along with C11orf30 and LRRC32 from chromosome 11q13.5, were studied in atopic dermatitis patients and control subjects from Bashkortostan. TLR1 (rs5743571 and rs5743604), TLR6 (rs5743794), and TLR10 (rs11466617) polymorphisms were associated with atopic dermatitis. The results supported the idea that innate immunity and polymorphisms of the TLR2-family genes play a substantial role in atopic dermatitis.     

A candidate gene association study for nine economically important traits in Italian Holstein cattle

We genotyped 58 single nucleotide polymorphisms (SNPs) in 25 candidate genes in about 800 Italian Holstein sires. Fifty‐six (minor allele frequency >0.02) were used to evaluate their association with single traits: milk yield (MY), milk fat yield (FY), milk protein yield (PY), milk fat percentage (FP), milk protein percentage (PP), milk somatic cell count (MSCC); and complex indexes: longevity, fertility and productivity–functionality type (PFT), using deregressed proofs, after adjustment for familial relatedness. Thirty‐two SNPs were significantly associated (proportion of false positives <0.05) with different traits: 16 with MSCC, 15 with PY, 14 with MY, 12 with PFT, eight with longevity, eight with FY, eight with PP, five with FP and two with fertility. In particular, a SNP in the promoter region of the PRLR gene was associated with eight of nine traits. DGAT1 polymorphisms were highly associated with FP and FY. Casein gene markers were associated with several traits, confirming the role of the casein gene cluster in affecting milk yield, milk quality and health traits. Other SNPs in genes located on chromosome 6 were associated with PY, PP, PFT, MY (PPARGC1A) and MSCC (KIT). This latter association may suggest a biological link between the degree of piebaldism in Holstein and immunological functions affecting somatic cell count and mastitis resistance. Other significant SNPs were in the ACACA, CRH, CXCR1, FASN, GH1, LEP, LGB (also known as PAEP), MFGE8, SRC, TG, THRSP and TPH1 genes. These results provide information that can complement QTL mapping and genome‐wide association studies in Holstein.     

Evolutionary origins of human apoptosis and genome-stability gene networks

Apoptosis is essential for complex multicellular organisms and its failure is associated with genome instability and cancer. Interactions between apoptosis and genome-maintenance mechanisms have been extensively documented and include transactivation-independent and -dependent functions, in which the tumor-suppressor protein p53 works as a ‘molecular node’ in the DNA-damage response. Although apoptosis and genome stability have been identified as ancient pathways in eukaryote phylogeny, the biological evolution underlying the emergence of an integrated system remains largely unknown. Here, using computational methods, we reconstruct the evolutionary scenario that linked apoptosis with genome stability pathways in a functional human gene/protein association network. We found that the entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2. Also, several critical nodes that entangle apoptosis and genome stability are cancer genes (e.g. ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6 and TP53), although their orthologs have arisen in different points of evolution. Our results demonstrate how genome stability and apoptosis were co-opted during evolution recruiting genes that merge both systems. We also provide several examples to exploit this evolutionary platform, where we have judiciously extended information on gene essentiality inferred from model organisms to human.