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

Background

Barley, globally the fourth most important cereal, provides food and beverages for humans and feed for animal husbandry. Maximizing grain yield under varying climate conditions largely depends on the optimal timing of flowering. Therefore, regulation of flowering time is of extraordinary importance to meet future food and feed demands. We developed the first barley nested association mapping (NAM) population, HEB-25, by crossing 25 wild barleys with one elite barley cultivar, and used it to dissect the genetic architecture of flowering time.

Results

Upon cultivation of 1,420 lines in multi-field trials and applying a genome-wide association study, eight major quantitative trait loci (QTL) were identified as main determinants to control flowering time in barley. These QTL accounted for 64% of the cross-validated proportion of explained genotypic variance (p_G). The strongest single QTL effect corresponded to the known photoperiod response gene Ppd-H1. After sequencing the causative part of Ppd-H1, we differentiated twelve haplotypes in HEB-25, whereof the strongest exotic haplotype accelerated flowering time by 11 days compared to the elite barley haplotype. Applying a whole genome prediction model including main effects and epistatic interactions allowed predicting flowering time with an unmatched accuracy of 77% of cross-validated p_G.

Conclusions

The elaborated causal models represent a fundamental step to explain flowering time in barley. In addition, our study confirms that the exotic biodiversity present in HEB-25 is a valuable toolbox to dissect the genetic architecture of important agronomic traits and to replenish the elite barley breeding pool with favorable, trait-improving exotic alleles.

     

Genetic variants in root architecture-related genes in a Glycine soja accession,a potential resource to improve cultivated soybean

Background

Root system architecture is important for water acquisition and nutrient acquisition for all crops. In soybean breeding programs, wild soybean alleles have been used successfully to enhance yield and seed composition traits, but have never been investigated to improve root system architecture. Therefore, in this study, high-density single-feature polymorphic markers and simple sequence repeats were used to map quantitative trait loci (QTLs) governing root system architecture in an inter-specific soybean mapping population developed from a cross between Glycine max and Glycine soja.

Results

Wild and cultivated soybean both contributed alleles towards significant additive large effect QTLs on chromosome 6 and 7 for a longer total root length and root distribution, respectively. Epistatic effect QTLs were also identified for taproot length, average diameter, and root distribution. These root traits will influence the water and nutrient uptake in soybean. Two cell division-related genes (D type cyclin and auxin efflux carrier protein) with insertion/deletion variations might contribute to the shorter root phenotypes observed in G. soja compared with cultivated soybean. Based on the location of the QTLs and sequence information from a second G. soja accession, three genes (slow anion channel associated 1 like, Auxin responsive NEDD8-activating complex and peroxidase), each with a non-synonymous single nucleotide polymorphism mutation were identified, which may also contribute to changes in root architecture in the cultivated soybean. In addition, Apoptosis inhibitor 5-like on chromosome 7 and slow anion channel associated 1-like on chromosome 15 had epistatic interactions for taproot length QTLs in soybean.

Conclusion

Rare alleles from a G. soja accession are expected to enhance our understanding of the genetic components involved in root architecture traits, and could be combined to improve root system and drought adaptation in soybean.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1334-6) contains supplementary material, which is available to authorized users.     

蔬菜作物积累硝酸盐的基因型差异及环境意义

城郊土壤富营养化已成为目前城郊农业生态系统可持续发展不可回避的环境问题之一,氮、磷养分富集是城郊土壤富营养化的重要表现形式,因土壤氮素积累而引起的蔬菜可食部位硝酸盐超标是一个亟待解决的技术难题.本文综述了不同蔬菜种及品种间吸收积累硝酸盐的基因型差异及其差异形成的生理生化机制,指出充分利用我国丰富的蔬菜种质资源,以植物吸收积累硝酸盐的基因型差异为理论基础,筛选弱吸收低积累蔬菜作物品种,是削减、控制蔬菜可食部位硝酸盐含量的关键性技术,有可能缓解城郊区脆弱生态环境条件下集约化生产对硝酸盐农艺阻控措施的依赖.     

Comparison of the chemical composition and the organoleptic profile of virgin olive oil from two wild and two cultivated Tunisian Olea europaea

With the aim to select new olive cultivars with superior physical and chemical properties than the cultivar Chemlali Sfax, the present study focused on the comparison of the chemical composition and the sensory profile of the virgin olive oils (VOOs) of two wild olive trees (Oleasters K and M) with those of VOOs obtained from Chemlali Sfax and Neb Jmel olive cultivars, all growing in the coastal region of Tunisia. Despite the variability in the chemical composition (fatty acids, pigments, and phenolic and volatile compounds) and the organoleptic profile of the VOOs of the oleasters and the cultivars, the quality indices (free fatty acids, peroxide value, and spectrophotometric indices K232 and K270) as well as the fatty acid composition of all VOOs studied met the commercial standards. Both the α-tocopherol and phenol contents varied between the genotypes. The Neb Jmel and Oleaster K VOOs had more than two times higher total phenol levels than the Chemlali Sfax and Oleaster M VOOs. Also the contents of volatile compounds differed between the olive oils studied. Chemlali Sfax and Oleaster K oils were more abundant in aldehydes, whereas Oleaster M VOO had higher contents of alcohols. These results were confirmed by a sensorial analysis showing that the later oil was deprived for consumption despite its abundance in α-tocopherol. In conclusion, the oleasters studied revealed to be interesting, since they produced oils with good quality characteristics in terms of minor compounds (phenols and volatiles) compared to the Chemlali Sfax cultivar.     

Seroprevalence of Toxoplasma gondii in wild boars (Sus scrofa leucomystax) and wild sika deer (Cervus nippon) in Gunma Prefecture, Japan

The ingestion of undercooked meat from wild animals can be a source of Toxoplasma gondii infection in humans and other animals. In this study, we determined the seroprevalence of T. gondii infection in 175 wild boars (Sus scrofa leucomystax) and 107 wild sika deer (Cervus nippon) hunted in 2004–2007 in Gunma Prefecture, Japan, by using a commercial latex agglutination test (LAT). Antibodies (LAT, 1:64 or higher) to T. gondii were found in 6.3% of wild boars and 1.9% of sika deer. This is the first record of T. gondii infection in wild deer in Japan, and deer and wild boar meat should be cooked well before human consumption.     

贵州葡萄属野生种光合特性的研究

为掌握野生葡萄种间和种内不同单株间的光合特性差异,利用Li-6400便携式光合测定系统测定了7种野生葡萄25个单株的光合参数.结果表明:野生葡萄种间光合特性差异明显,美丽葡萄净光合速率最高,其次是刺葡萄,腺枝葡萄的净光合速率最低.野生葡萄种内不同单株间的光合指标多样性丰富,单株间光合特性差异最大的是葛藟葡萄;种内不同单株间原产地气候条件相似,其光合特性差异较小,而原产地气候差异大的单株光合特性差异也大;野生葡萄的光合速率调控机制多样,非气孔因素调控在野生葡萄种群内非常普遍.     

黄麻两个栽培种及其野生类型与三个近缘种的核型分析

本研究选取黄麻属（Corchorus）2个栽培品种及其4个野生类型和3个野生近缘种为材料,采用常规根尖压片法对黄麻属供试材料的染色体数目和核型进行研究。结果表明：染色体数目均为2n=14。核型公式分别为：宽叶长果（长果黄麻栽培种）2n=2x=14=14m(4SAT);南阳野生长果（长果黄麻野生类型）2n=2x=14=14m(2SAT);坦桑尼亚野生长果（长果黄麻野生类型）2n=2x=14=2M+12m;闽麻5号（圆果黄麻栽培种）2n=2x=14=12m+2sm;爱店野生圆果（圆果黄麻野生类型）2n=2x=14=14m ;廉江野生圆果（圆果黄麻野生类型） 2n=2x=14=4M+10m;假黄麻（黄麻属野生近缘种）2n=2x=14=2M+12m;假长果（黄麻属野生近缘种）2n=2x=14=2M+12m;甜麻（黄麻属野生近缘种）2n=2x=14=14m。其中除了宽叶长果核型分类为1B外,其他的都为1A型。本文还讨论了黄麻野生近缘种甜麻的分类学地位。     

The sexual function of wallowing in male wild boar (Sus scrofa)

The wild boar (Sus scrofa) is a medium-sized ungulate that produces a large variety of marks. Traditionally, wallowing is an activity that has fundamentally been related to several processes such as thermoregulation, reduction in the number of ectoparasites or disinfection of wounds in the skin of males resulting from fights to reach females. In this study, I analysed another possible function of wallowing in free-ranging wild boar populations when temperatures are low and parasitic numbers are not significant. The results indicate that during the sampling time, from October to February, the number of wild boars with a mud layer on their skin was 47, out of a total of 558 wild boar analysed. Of these 47 wild boars, 44 were males and within this group, 40 individuals were adult males. The wallowed males were bigger and older than non-wallowed males hunted at the same time. In addition, I found that males wallowed mainly during autumn (90.9% of all cases). In the total number of wild boars analysed, I did not notice individuals with wounds resulting from fights other than from the hunting day. On the other hand, the analysis of the females reproductive systems indicated that the rut period took place during the last days of October and the first days of November. From these results, the coincidence of the rut period with the maximum of wallowing in adult males could be indicative of a sexual function of this activity.     

Variability and structure of natural populations of Elymus caninus (L.) L. based on morphology

Great variability involving 36 quantitative and 31 qualitative characters, as well as the habitats occupied has been shown in 18 populations of Elymus caninus from Poland, based on the detailed population and statistical analyses of morphological characters. The variability of these characters proves that the intraspecific units which have been distinguished on the basis of these characters do not have systematic significance. The two morphotypes of E. caninus (pauciflorum and caninus) described in this study will provide the basis for further genetic studies aimed at establishing their significance for considerations in the systematics of the species.It is the first paper from the series: Biodiversity of wild Triticeae (Poaceae) in Poland.     

Vegetation: A source of air fungal bio-contaminant

Airborne fungal counts and types were examined in three selected regions in Egypt. Two of the sampling sites are rural areas, one cultivated with chamomile and the second with vegetable. The third site is located in an urban area. A sedimentation method was used to isolate airborne fungal spores. Airborne fungal spore counts averaged 71\pm 19, 64\pm 14 and 175\pm 79 cfu/p/h in the urban, vegetable and chamomile growing areas, respectively. A total of 1486 fungal colonies belonging to 32 genera were identified. Alternaria (7.5–59.9%), Aspergillus (11.2–38.9%), Penicillium (9.5–15%) and Cladosporium (7.78–17.5%) were the predominant fungal genera found in all sampling sites. Alternaria (42–59.9%) and Aspergillus (38.9%) were the common fungal genera in the cultivated and urban areas, respectively. Vegetation is considered the main source of Alternaria, whereas Aspergillus, Penicillium and Cladosporium are related to local microenvironments and urbanization. Acremonium, Aureobasidium, Botrytis, Beauveria, Chlamydomyces, Chalara, Curvularia, Fusarium, Geotrichum, Trichothecium, Oidiodendron, Scopulariopsis, Spicaria, Stachybotrys chartarum, Torula and Thamnidium, were only detected in low percentages (0.11–1.8%) in the cultivated areas. Vegetation adds different fungal types into the air and their numbers vary according to vegetation type and weather conditions. Airborne fungal counts increased with temperature and decreased with rainfall and relative humidity. Airborne fungal spores have many implications in the spread of human and plant diseases. The presence of fungal spores in air, in spite of their counts, may raise arguments about their role in health complaints in a particular region, „i.e., the fungal concentration may be low but the predominant aeroallergen may be dangerous”.