Genetic diversity and structure of the portuguese pear (Pyrus communis L.) germplasm

A rich heritage of traditional pear varieties is kept in national Portuguese collections. Out of these varieties, “Rocha” dominates national pear production. Although a noticeable phenotypic variation among clones of this variety has been reported, little is known about its genetic variability, as to date molecular studies have been performed on a single “Rocha” clone. Eleven Simple Sequence Repeats (SSR) markers were used to assess the genetic diversity of 130 local cultivars, 80 of them being “Rocha” clones. The results allowed the di erentiation of 75 genotypes of which 29 are “Rocha”. Three synonyms groups and four homonymous groups of other local varieties were confirmed. A Bayesian model-based clustering approach identified two distinct clusters. Using flow cytometry, six cultivars were found to be triploids. These results show high genetic variability among “Rocha” clones. In conclusion, there is a need for di erent “Rocha” clones to be preserved to enable the correct selection of the multiplication materialinfo:eu-repo/semantics/publishedVersio

Genome-wide clonal variability in European pear “Rocha” using high-throughput sequencing

Pears (Pyrus) are one of the most economically important fruits worldwide. The Pyrus genus is characterized by a high degree of genetic variability between species and interspecific hybrids, and several studies have been performed to assess this variability for both cultivated and wild accessions. These studies have mostly been limited by the resolving power of traditional molecular markers, although in the recent past the availability of reference genome sequences or SNP arrays for pear have enhanced the capability of high-resolution genomics studies. These tools can also be applied to better understand the intra-varietal (or clonal) variability in pear. Here we report the first high resolution genomics analysis of a pear clonal population using whole genome sequencing (WGS). Results showed unique signatures for the accumulation of mutations and transposable element insertions in each clone, which are likely related to their history of propagation and cultivation. The nucleotide diversity remained low in the clonal collection with the exception of few genomic windows, suggesting that balancing selection may be occurring. These windows included mainly genes related to plant fertility. Regions with higher mutational load were partially associated with transcription factors, probably reflecting the distinctive phenotypes in the collection. The annotation of variants also revealed the theoretical disruption of relevant genes in pear. Taken together, the results from this study show that pear clones accumulate mutations differently, and that those mutations can play a role on pear phenotypes, meaning that the study of pear clonal populations can be relevant in genetic studies, mainly when comparing with traditional association studies.info:eu-repo/semantics/publishedVersio

Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp.) Landraces from Portugal and Mozambique

Abstract: Cowpea (Vigna unguiculata (L.) Walp.) is currently a legume crop of minor importance in Europe but a highly relevant staple crop in Africa and the second most cultivated legume in Mozambique. In Portugal and Mozambique, cowpea’s phenotypic and genetic variation has been maintained locally by farmers in some areas. We used the molecular markers SSR, SilicoDArT and SNP to analyze the genetic diversity and population structure of 97 cowpea accessions, mainly from Portugal (Southern Europe) and Mozambique (Southern Africa). As far as we know, this is the first time that the genetic variation and the relationship between cowpea landraces collected in Portugal with those originated in Mozambique is reported. Despite the shared historical past, the Portuguese landraces did not share a common genetic background with those from Mozambique, and two different gene pools were revealed. Knowledge of the genetic structure of cowpea landraces offers an opportunity for individual selection within landraces adapted to particular eco-physiological conditions and suggests the existence of a valuable gene pool for exploitation in future Portugal-PALOP (Portuguese-speaking African countries) cowpea breeding programs.info:eu-repo/semantics/publishedVersio

Comparative transcriptomic response of two Pinus species to infection with the pine wood nematode Bursaphelenchus xylophilus

Pine wilt disease (PWD) caused by pine wood nematode (PWN), Bursaphelenchus xylophilus, is a serious threat to global forest populations of conifers, in particular Pinus spp. Recently, the presence of PWN was reported in dead Yunnan pine (Pinus yunnanensis) trees under natural conditions. To further understand the potential impact caused by PWN in Yunnan pine populations, a transcriptional profiling analysis was performed over di erent time points (0 hours (h), 6 h, 24 h, 48 h, and 7 days) after PWN inoculation. A total of 9961 di erentially expressed genes were identified after inoculation, which suggested a dynamic response against the pathogen, with a more intense pattern at 48 h after inoculation. The results also highlighted a set of biological mechanisms triggered after inoculation that provide valuable information regarding the response of Yunnan pine to PWN infection. When compared with maritime pine (Pinus pinaster), the Yunnan pine response was less complex and involved a smaller number of di erentially expressed genes, which may be associated with the increased degree of resistance to PWN displayed by Yunnan pine. These results revealed di erent strategies to cope with PWN infection by these two pine species, which display contrasting degrees of susceptibility, especially in the timely perception of the infection and response magnitudeinfo:eu-repo/semantics/publishedVersio

Genetic Diversity and Population Structure of Wild Beets (Beta spp.) from the Western Iberian Peninsula and the Azores and Madeira Islands

In this work, using simple sequence repeat (SSR) markers, we present new insights into the genetic diversity, differentiation, and structure of Beta vulgaris subsp. maritima of western Iberia and the Azores and Madeira islands and of B. macrocarpa from southern Portugal. B. macrocarpa occurs only in southern Portugal and frequently in sympatry with B. vulgaris subsp. maritima, showing genetic introgression. B. macrocarpa has a better-defined structure than B. vulgaris subsp. maritima, which has a high degree of admixture. A great differentiation (FST ranging from 0.277 to 0.184) was observed among the northern populations of B. vulgaris subsp. maritima. In contrast, only a small differentiation (FST ranging from 0.000 to 0.026) was detected among the southern B. vulgaris subsp. maritima populations. The inland B. vulgaris subsp. maritima populations (“RIO” and “VMT”) are distinct from each other, which also occurs with the two islands’ populations (“MAD” and “AZO”). The existence of two distinct Atlantic Sea currents can explain the fact that Madeira is related to the southern populations, while the Azores is related to the northern populations. We consider that understanding the relationships existing within Beta spp. is key to future genetic studies and for the establishment of conservation measures. Our results show that the southern coastal areas of Portugal should be considered as a potential site for in situ conservation of the beet wild relatives. Special attention is needed in what concerns B. macrocarpa because this is a rare species that also occurs in a sympatric relationship with B. vulgaris subsp. maritimainfo:eu-repo/semantics/publishedVersio

How to Improve Already Improved Cowpea—Terminal Drought

Cowpea’s (Vigna unguiculata) heat and drought resistance, high protein content, and nitrogen-fixing ability place this crop within the three dimensions of sustainable development; social, economic, and environmental. Modern disregard for landrace causes genetic variability loss, compromising breeding efforts in the context of climate changes. To contribute to the evaluation of Portuguese cowpea germplasm, several landraces were compared with a commercial variety (CV) in terms of productivity and physiological responses to drought. Despite a clear effect of stress in photosynthesis, there were no differences between the CV and landraces. However, under drought, higher relative chlorophyll content (SPAD) was kept for longer in the CV. All showed a marked decrease in productivity (60–70%) under stress, but the CV produced bigger and heavier seeds. The similar results between CV and landraces reflect the significance of the pragmatic selection of on-farm conserved landraces under Mediterranean climate. Molecular characterization of genetic diversity is on course using microsatellites

Genetic Diversity and Population Structure of Cowpea (<i>Vigna unguiculata</i> (L.) Walp.) Landraces from Portugal and Mozambique

Cowpea (Vigna unguiculata (L.) Walp.) is currently a legume crop of minor importance in Europe but a highly relevant staple crop in Africa and the second most cultivated legume in Mozambique. In Portugal and Mozambique, cowpea’s phenotypic and genetic variation has been maintained locally by farmers in some areas. We used the molecular markers SSR, SilicoDArT and SNP to analyze the genetic diversity and population structure of 97 cowpea accessions, mainly from Portugal (Southern Europe) and Mozambique (Southern Africa). As far as we know, this is the first time that the genetic variation and the relationship between cowpea landraces collected in Portugal with those originated in Mozambique is reported. Despite the shared historical past, the Portuguese landraces did not share a common genetic background with those from Mozambique, and two different gene pools were revealed. Knowledge of the genetic structure of cowpea landraces offers an opportunity for individual selection within landraces adapted to particular eco-physiological conditions and suggests the existence of a valuable gene pool for exploitation in future Portugal-PALOP (Portuguese-speaking African countries) cowpea breeding programs