Characterization of polyploid wheat genomic diversity using a high‐density 90 000 single nucleotide polymorphism array

High‐density single nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for studying genomic patterns of diversity, inferring ancestral relationships between individuals in populations and studying marker–trait associations in mapping experiments. We developed a genotyping array including about 90 000 gene‐associated SNPs and used it to characterize genetic variation in allohexaploid and allotetraploid wheat populations. The array includes a significant fraction of common genome‐wide distributed SNPs that are represented in populations of diverse geographical origin. We used density‐based spatial clustering algorithms to enable high‐throughput genotype calling in complex data sets obtained for polyploid wheat. We show that these model‐free clustering algorithms provide accurate genotype calling in the presence of multiple clusters including clusters with low signal intensity resulting from significant sequence divergence at the target SNP site or gene deletions. Assays that detect low‐intensity clusters can provide insight into the distribution of presence–absence variation (PAV) in wheat populations. A total of 46 977 SNPs from the wheat 90K array were genetically mapped using a combination of eight mapping populations. The developed array and cluster identification algorithms provide an opportunity to infer detailed haplotype structure in polyploid wheat and will serve as an invaluable resource for diversity studies and investigating the genetic basis of trait variation in wheat.     

QTLs for Woolly Poplar Aphid (Phloeomyzus passerinii L.) Resistance Detected in an Inter-Specific Populus deltoides x P. nigra Mapping Population

The genus Populus represents one of the most economically important groups of forest trees. It is composed by approximately 30 species used for wood and non-wood products, phytoremediation and biomass. Poplar is subjected to several biological and environmental threats although, compared to annual crops, we know far less about the genetic bases of biotic stress resistance. Woolly poplar aphid (Phloeomyzus passerinii) is considered a main pest of cultivated poplars in European and American countries. In this work we present two high density linkage maps in poplar obtained by a genotyping by sequencing (GBS) approach and the identification of QTLs involved in Ph. passerinii resistance. A total of 5,667 polymorphic markers (5,606 SNPs and 61 SSRs) identified on expressed sequences have been used to genotype 131 plants of an F1 population P ×canadensis obtained by an interspecific mate between Populus deltoides (resistant to woolly poplar aphid) and Populus nigra (susceptible to woolly poplar aphid). The two linkage maps, obtained following the two-way pseudo-testcross mapping strategy, have been used to investigate the genetic bases of woolly poplar aphid resistance. One major QTL and two QTLs with minor effects (mapped on LGV, LGXVI and LG XIX) explaining the 65.8% of the genetic variance observed in the progeny in response to Ph. passerinii attack were found. The high density coverage of functional markers allowed the identification of three genes belonging to disease resistance pathway as putative candidates for P. deltoides resistance to woolly poplar aphid. This work is the first report on genetic of woolly poplar aphid genetic resistance and the resistant loci associated markers identified represent a valuable tool in resistance poplar breeding programs.     

Effects of growth stage and hardening conditions on the association between frost resistance and the expression of the cold-induced protein COR14b in barley

Sowing date, being determinant for growth stage, may play a decisive role in optimising freezing resistance of winter annual plants. In cereal species, in spite of the abundant literature analysing the factors responsible for the acquisition of frost resistance through the cold hardening process, the involvement of the growth stage per se, has been seldom considered, especially at the earlier vegetative phases. In this work the contribution of growth stage in determining resistance to freezing temperature has been analysed in field and growth chamber experiments using winter and spring barley cultivars exposed to different hardening conditions. Field damage was assessed twice during winter on plants sown at three different dates. In the growth chamber experiments several acclimation treatments at 11/7 and/or 3/1 °C (day/night) were simulated. In both field and laboratory experiments the development of cold acclimation was monitored by means of a COR14b specific antibody, since in previous studies the expression of COR14b was found genetically linked to frost resistance. The lowest resistance, found in the youngest plants and in spring cultivars, however, was not always associated with the lowest level of COR14b accumulation. COR14b accumulation correlated with frost resistance at the earlier field sampling date and in plants grown at 11/7 °C. In a following phase of the hardening process (second sampling in field and 4 weeks at 3/1 °C in growth chamber) the accumulation of COR14b was independent of plant stage and genotype, showing no association with freezing resistance. Results suggest that growth stage is crucial for the achievement of maximal resistance in barley, but not for COR14b expression.     

Insight into durum wheat <Emphasis Type="Italic">Lpx-B1</Emphasis>: a small gene family coding for the lipoxygenase responsible for carotenoid bleaching in mature grains

Background  

The yellow colour of pasta products is one of the main criteria used by consumers to assess pasta quality. This character is due to the presence of carotenoid pigments in semolina. During pasta processing, oxidative degradation of carotenoid pigments occurs mainly due to lipoxygenase (LOX). In durum wheat (Triticum durum Desf.), two Lpx-1 genes have been identified on chromosome 4B, Lpx-B1.1 and Lpx-B1.2, and evidences have been reported that the deletion of Lpx-B1.1 is associated with a strong reduction in LOX activity in semolina. In the present study, we characterised the Lpx-B1 gene family identified in a durum wheat germplasm collection and related the distribution and expression of the Lpx-B1 genes and alleles to variations in LOX activity in the mature grains.