Genome-wide association study dissects the genetic control of plant height and branch number in response to low-phosphorus stress in Brassica napus

Background and AimsOilseed rape (Brassica napus) is one of the most important oil crops worldwide. Phosphorus (P) deficiency severely decreases the plant height and branch number of B. napus. However, the genetic bases controlling plant height and branch number in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for plant height and branch number by genome-wide association study (GWAS) and determine low-P-tolerance haplotypes.MethodsAn association panel of B. napus was grown in the field with a low P supply (P, 0 kg ha⁻¹) and a sufficient P supply (P, 40 kg ha⁻¹) across 2 years and plant height and branch number were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of plant height and branch number at two contrasting P supplies.Key ResultsA total of 2127 SNPs were strongly associated (P < 6·25 × 10⁻⁰⁷) with plant height and branch number at two P supplies. There was significant correlation between phenotypic variation and the number of favourable alleles of associated loci on chromosomes A10 (chrA10_821671) and C08 (chrC08_27999846), which will contribute to breeding improvement by aggregating these SNPs. BnaA10g09290D and BnaC08g26640D were identified to be associated with chrA10_821671 and chrC08_27999846, respectively. Candidate gene association analysis and haplotype analysis showed that the inbred lines carrying ATT at BnaA10g09290Hap1 and AAT at BnaC08g26640Hap1 had greater plant height than lines carrying other haplotype alleles at low P supply.ConclusionOur results demonstrate the power of GWAS in identifying genes of interest in B. napus and provided insights into the genetic basis of plant height and branch number at low P supply in B. napus. Candidate genes and favourable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus.     

Reproductive success and variation in floral traits in the Iberian Peninsula endemic white campion <Emphasis Type="Italic">Silene marizii</Emphasis> (Caryophyllaceae)

Silene marizii (Caryophyllaceae) is a schizoendemism of the west Iberian Peninsula. The correlation between the evolution of reproductive success (as measured in terms of fruit set and seed production) and five floral traits (peduncle length, calyx length, calyx width, petal limb length, and petal limb width) was investigated in five populations of S. marizii, taking into account both intra-populational and inter-populational variability. The populations studied represented the different habitats of S. marizii over its area of distribution. None of the five traits examined was significantly and positively correlated with the number of seeds produced by the flower. An analysis was also made of how floral morphology varies with the position of the flower in the inflorescence in the five populations. The populations from higher altitudes (Caramulhino, Puerto de Menga and Peña de la Cruz) had larger peduncles, calices and petal limbs than those living at lower altitudes (Sabugal and Mangualde) All five morphometric traits, plus the number of ovules per ovary, varied significantly between flower positions on the same plant and among populations.     

Study on the evolution of the grande retrotransposon in the zea genus

The study of Grande retrotransposon (RTN) variation reported here comprises the intrinsic element variability and the changes that element insertion provokes in the Zea genome, including its abundance among species. Sequence analysis of a defined long-terminal repeat (LTR) region from Grande RTN revealed a high level of sequence divergence since no identical sequences were found among the 65 clones examined that belong to different Zea species or maize inbred lines. Average diversity values within accessions ranged from 0.17 to 0.37 substitutions per nucleotide. Phylogenetic analysis revealed a lack of concordance between the phylogenetic tree obtained from LTR sequences and the conventional taxonomic tree, suggesting that different subfamilies of Grande elements existed before Zea speciation. When sequence-specific amplification polymorphism (SSAP) marker data, which combines genomic and RTN variation, are used, the derived trees reflect the established species phylogeny and allow, as well, differentiating among some maize lines. Finally, the evaluation of Grande abundance, using different element probes in all the Zea species but Z. luxurians, revealed around 5,700 copies per haploid genome in all the diploid species examined, indicating a similar expansion process of Grande in all the Zea genomes. This number of copies represents in all cases around a 3% of the genome, which implies that Grande RTN is an important component of the maize genome. The copy number ratio LTR/gag is around 2 in all the species analyzed, indicating that overwhelming majority of elements have internal region. Thus, mechanisms such as homologous recombination between LTRs of a single RTN, which would remove the internal region and one LTR, leaving behind a single recombinant LTR, seems not to be active in maize for Grande RTN.     

Host genetic risk factors for community-acquired pneumonia

This study was conducted to establish the contribution of genetic host factors in the susceptibility to community acquired pneumonia (CAP) in the Russian population. Patients with CAP (n = 334), volunteers without a previous history of CAP, constantly exposed to infectious agents, control A group (n = 141) and a second control group B consisted of healthy persons (n = 314) were included in the study. All subjects were genotyped for 13 polymorphic variants in the genes of xenobiotics detoxification CYP1A1 (rs2606345, rs4646903, and rs1048943), GSTM1 (Ins/del), GSTT1 (Ins/del), ABCB1 rs1045642); immune and inflammation response IL-6 (rs1800795), TNF-a (rs1800629), MBL2 (rs7096206), CCR5 (rs333), NOS3 (rs1799983), angiotensin-converting enzyme ACE (rs4340), and occlusive vascular disease/hyperhomocysteinemia MTHFR (rs1801133). Seven polymorphic variants in genes CYP1A1, GSTM1, ABCB1, NOS3, IL6, CCR5 and ACE were associated with CAP. For two genes CYP1A1 and GSTM1 associations remained significant after correction for multiple comparisons. Multiple analysis by the number of all risk genotypes showed a highly significant association with CAP (P = 2.4 × 10^− 7, OR = 3.03, 95% CI 1.98–4.64) with the threshold for three risk genotypes. Using the ROC-analysis, the AUC value for multi-locus model was estimated as 68.38.     

Ploidy in the alpine sedge Kobresia pygmaea (Cyperaceae) and related species: combined application of chromosome counts,new microsatellite markers and flow cytometry

Polyploidy is a fundamental mechanism in evolution, but is hard to detect in taxa with agmatoploidy or aneuploidy. We tested whether a combination of chromosome counting, microsatellite analyses and flow cytometric measurements represents a suitable approach for the detection of basic chromosome numbers and ploidy in Kobresia (Cyperaceae). Chromosome counting resulted in 2n = 64 for Kobresia pygmaea and K. cercostachys, 2n = 58 and 64 for K. myosuroides, and 2n = 72 for K. simpliciuscula. We characterized eight microsatellite loci for K. pygmaea, which gave a maximum of four alleles per individual. Cross‐species amplification was tested in 26 congeneric species and, on average, six of eight loci amplified successfully. Using flow cytometry, we confirmed tetraploidy in K. pygmaea. Basic chromosome numbers and ploidy were inferred from chromosome counts and the maximum number of alleles per locus. We consider the basic numbers as x = 16 and 18, with irregularities derived from agmatoploidy and aneuploidy. Across all Kobresia taxa, ploidy ranged from diploid up to heptaploid. The combination of chromosome counts and microsatellite analyses is an ideal method for the determination of basic chromosome numbers and for inferring ploidy, and flow cytometry is a suitable tool for the identification of deviating cytotypes. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 22–35.     

Unilateral and bilateral hybridization barriers in inter-series crosses of 4x 2EBN Solanum stoloniferum, S. pinnatisectum, S. cardiophyllum, and 2x 2EBN S. tuberosum haploids and haploid-species hybrids

Wild Mexican potato species are an important untapped source of useful variation for potato improvement. Introgression methods such as 2n gametes, chromosome doubling, and crossing with disomic 4x 2 endosperm balance number (EBN) bridge species have been used to overcome post-zygotic endosperm failure according to the EBN hypothesis. Stylar barriers can prevent zygote formation, bilaterally when zygote formation is blocked in both directions of the cross or unilaterally when zygote formation is blocked in self incompatible (SI) × self compatible (SC) crosses. In several Solanaceae species, the S-locus for SI has been implicated in interspecific incompatibility. The objectives of this research were to determine if: (1) disomic 4x 2EBN Solanum stoloniferum can be used as a bridge species for introgression of the Mexican 2x 1EBN species Solanum cardiophyllum and Solanum pinnatisectum, (2) pre- and/or post-zygotic barriers limit hybridization among EBN compatible Solanum inter-series crosses, and (3) reproductive barriers act unilaterally or bilaterally. Fruit formation and seed set was recorded for inter-pollinations of S. stoloniferum, 4x 2EBN chromosome doubled S. cardiophyllum and S. pinnatisectum, and 2x 2EBN S. tuberosum haploids (HAP) or haploid-species hybrids (H-S). In vivo pollen tube growth was analyzed for each cross combination with fluorescence microscopy. Attempts to create bridge hybrids between S. stoloniferum, and S. cardiophyllum or S. pinnatisectum were not successful. Pre- and post-zygotic barriers prevented seed formation in crosses involving S. cardiophyllum and S. pinnatisectum. Self compatibility in S. stoloniferum and S. pinnatisectum suggests that the S-locus does not contribute to the stylar barriers observed with these species. Alternatively, the presence of functional and nonfunctional (SC) S-alleles may explain interspecific incompatibility in intra- and inter-ploidy crosses. A non-stylar unilateral incongruity was discovered in H-S/HAP × S. stoloniferum crosses, indicating either a post-zygotic barrier, or a pre-zygotic barrier acting at or within the ovary. Furthermore, lack of S. stoloniferum pollen rejection may occur through absence of S. stoloniferum pollen-active genes needed to initiate pollen rejection, or through competitive interaction in S-locus heterozygous S. stoloniferum pollen. Introgression strategies using these species would benefit potato breeding by introducing genetic diversity for several traits simultaneously through co-current introgression.     

Crop row spacing and its influence on the partitioning of evapotranspiration by winter-grown wheat in Northern Syria

A study was conducted during the 1996–97 crop growth season at ICARDA in northern Syria, to investigate the influence of wheat canopy architecture on the partitioning of moisture between soil evaporation and crop transpiration, on a soil with high hydraulic conductivity. The study was conducted on the long-term two course wheat-lentil rotation trial, established on a swelling clay soil (Calcixerollic xerochrept). The wheat canopy architecture was manipulated by sowing the crop at either of two row-spacings, 0.17 or 0.30 m, both at a constant sowing rate equivalent to 120 kg ha^–1. In this study, evapotranspiration from the crop was inferred from changes in soil moisture content over time, evaporation and rainfall interception were measured daily using microlysimetry, drainage was estimated as being the difference between potential daily evapotranspiration, and the evapotranspiration estimated from the soil water deficit. Between sowing and day 80 (tillering stage), evapotranspiration was calculated to consist mainly of soil evaporation. However, after day 80, transpiration became an increasingly dominant component of evapotranspiration. For both row-spacings, cumulative evapotranspiration over the season was approximately 373 mm. In the narrow-row crop, transpiration and soil evaporation were approximately 185 mm and 183 mm of water respectively. Conversely for the wide row-spaced crop, 172 mm of water was transpired while about 205 mm of water evaporated from the soil surface. While green leaf area index did not differ between row-spacings, the architecture of the crops as a result of sowing affected solar radiation penetration such that more incident radiation was intercepted at the soil surface of the wide row-spaced crop. This is likely to have made some contribution to the elevated levels of evaporation from the soil beneath the canopy of the wide-sown crop.