Microsatellites for the genus Cucurbita and an SSR-based genetic linkage map of Cucurbita pepo L.

Until recently, only a few microsatellites have been available for Cucurbita, thus their development is highly desirable. The Austrian oil-pumpkin variety Gleisdorfer Ölkürbis (C. pepo subsp. pepo) and the C. moschata cultivar Soler (Puerto Rico) were used for SSR development. SSR-enriched partial genomic libraries were established and 2,400 clones were sequenced. Of these 1,058 (44%) contained an SSR at least four repeats long. Primers were designed for 532 SSRs; 500 primer pairs produced fragments of expected size. Of these, 405 (81%) amplified polymorphic fragments in a set of 12 genotypes: three C. moschata, one C. ecuadorensis, and eight C. pepo representing all eight cultivar groups. On an average, C. pepo and C. moschata produced 3.3 alleles per primer pair, showing high inter-species transferability. There were 187 SSR markers detecting polymorphism between the USA oil-pumpkin variety “Lady Godiva” (O5) and the Italian crookneck variety “Bianco Friulano” (CN), which are the parents of our previous F2 mapping population. It has been used to construct the first published C. pepo map, containing mainly RAPD and AFLP markers. Now the updated map comprises 178 SSRs, 244 AFLPs, 230 RAPDs, five SCARs, and two morphological traits (h and B). It contains 20 linkage groups with a map density of 2.9 cM. The observed genome coverage (Co) is 86.8%

Syntenic relationships between cucumber (Cucumis sativus L.) and melon (C. melo L.) chromosomes as revealed by comparative genetic mapping

<p>Abstract</p> <p>Background</p> <p>Cucumber, <it>Cucumis sativus </it>L. (2n = 2 × = 14) and melon, <it>C. melo </it>L. (2n = 2 × = 24) are two important vegetable species in the genus <it>Cucumis </it>(family Cucurbitaceae). Both species have an Asian origin that diverged approximately nine million years ago. Cucumber is believed to have evolved from melon through chromosome fusion, but the details of this process are largely unknown. In this study, comparative genetic mapping between cucumber and melon was conducted to examine syntenic relationships of their chromosomes.</p> <p>Results</p> <p>Using two melon mapping populations, 154 and 127 cucumber SSR markers were added onto previously reported F₂- and RIL-based genetic maps, respectively. A consensus melon linkage map was developed through map integration, which contained 401 co-dominant markers in 12 linkage groups including 199 markers derived from the cucumber genome. Syntenic relationships between melon and cucumber chromosomes were inferred based on associations between markers on the consensus melon map and cucumber draft genome scaffolds. It was determined that cucumber Chromosome 7 was syntenic to melon Chromosome I. Cucumber Chromosomes 2 and 6 each contained genomic regions that were syntenic with melon chromosomes III+V+XI and III+VIII+XI, respectively. Likewise, cucumber Chromosomes 1, 3, 4, and 5 each was syntenic with genomic regions of two melon chromosomes previously designated as II+XII, IV+VI, VII+VIII, and IX+X, respectively. However, the marker orders in several syntenic blocks on these consensus linkage maps were not co-linear suggesting that more complicated structural changes beyond simple chromosome fusion events have occurred during the evolution of cucumber.</p> <p>Conclusions</p> <p>Comparative mapping conducted herein supported the hypothesis that cucumber chromosomes may be the result of chromosome fusion from a 24-chromosome progenitor species. Except for a possible inversion, cucumber Chromosome 7 has largely remained intact in the past nine million years since its divergence from melon. Meanwhile, many structural changes may have occurred during the evolution of the remaining six cucumber chromosomes. Further characterization of the genomic nature of <it>Cucumis </it>species closely related to cucumber and melon might provide a better understanding of the evolutionary history leading to modern cucumber.</p

Exploration of Shared Genetic Architecture Between Subcortical Brain Volumes and Anorexia Nervosa

In MRI scans of patients with anorexia nervosa (AN), reductions in brain volume are often apparent. However, it is unknown whether such brain abnormalities are influenced by genetic determinants that partially overlap with those underlying AN. Here, we used a battery of methods (LD score regression, genetic risk scores, sign test, SNP effect concordance analysis, and Mendelian randomization) to investigate the genetic covariation between subcortical brain volumes and risk for AN based on summary measures retrieved from genome-wide association studies of regional brain volumes (ENIGMA consortium, n = 13,170) and genetic risk for AN (PGC-ED consortium, n = 14,477). Genetic correlations ranged from − 0.10 to 0.23 (all p > 0.05). There were some signs of an inverse concordance between greater thalamus volume and risk for AN (permuted p = 0.009, 95% CI: [0.005, 0.017]). A genetic variant in the vicinity of ZW10, a gene involved in cell division, and neurotransmitter and immune system relevant genes, in particular DRD2, was significantly associated with AN only after conditioning on its association with caudate volume (pFDR = 0.025). Another genetic variant linked to LRRC4C, important in axonal and synaptic development, reached significance after conditioning on hippocampal volume (pFDR = 0.021). In this comprehensive set of analyses and based on the largest available sample sizes to date, there was weak evidence for associations between risk for AN and risk for abnormal subcortical brain volumes at a global level (that is, common variant genetic architecture), but suggestive evidence for effects of single genetic markers. Highly powered multimodal brain- and disorder-related genome-wide studies are needed to further dissect the shared genetic influences on brain structure and risk for AN

Divergência genética entre acessos de batata-doce utilizando caracteres fenotípicos de raiz Genetic divergence among sweet potato accessions based on root traits

Estudos de quantificação da divergência genética entre acessos e caracterização dos recursos genéticos têm sido de grande importância em programas de melhoramento, auxiliando na identificação de genitores e no conhecimento do material genético disponível. Os objetivos do presente trabalho foram: (1) avaliar os acessos de batata-doce pertencentes ao banco de germoplasma da Embrapa com base em caracteres de raiz; (2) calcular a importância relativa dos caracteres morfo-agronômicos quantitativos na discriminação dos acessos e, (3) obter indicações das combinações híbridas mais promissoras para cruzamentos. Foi avaliada uma coleção de 11 clones pertencentes ao Banco Ativo de Germoplasma da Embrapa por meio de um experimento conduzido na Embrapa SPM/EN, em Canoinhas-SC. Os acessos foram cultivados em condições de campo no delineamento em blocos ao acaso com quatro repetições, onde a parcela experimental foi composta por 10 plantas. As plantas de cada parcela foram colhidas e avaliadas para 12 caracteres fenotípicos de raiz. O estudo indicou que os caracteres número e massa total de raízes e peso específico foram os que mais contribuíram para a divergência genética. A maioria dos acessos é bastante similar quanto aos caracteres quantitativos avaliados. Porém, há a possibilidade de ganhos com a heterose, geração de variabilidade genética e de progênies superiores cruzando-se os acessos dos diferentes grupamentos formados; pois os genótipos mais contrastantes '1228', '051-1' e '1270' foram agrupados entre os melhores para várias características como massa e número total de raízes, massa comercial de raízes; os dois primeiros apresentaram elevado peso específico e o '1270' apresentou coloração alaranjada intensa, indicativo de alto teor de &#946;-caroteno.<br>The estimation of the genetic divergence among accessions of a germplasm bank, as well as their characterization are very important in breeding programs in order to identify the best parental genotypes and to provide a better understanding of the available plant genetic resources. Considering this information, the objectives of this research were: (1) evaluate the sweet potato plant accessions of Embrapa Germplasm Bank based on root traits; (2) estimate the relative importance of quantitative morphoagronomic characters in the genotype discrimination; and (3) find out promising hybrid combinations for crosses. Then, 11 sweet potato clones from Embrapa Germplasm Bank were evaluated in a trial at Embrapa SPM/EN Canoinhas, Brazil. The genotypes were cultivated in field conditions on a randomized blocks experimental design with four replications; the experimental plot was composed of 10 plants. In each experimental plot the plants were harvested and 12 characteristics of the roots were evaluated. The total number and mass of roots, and the specific gravity were the characteristics with the greatest influence on the genetic divergence. Most of the evaluated genotypes were closely related considering their quantitative characteristics. However, it is possible to obtain useful gains with heterosis and the generation of superior progenies, through crosses between genotypes from the different groups; because the most contrasting genotypes '1228', '051-1' and '1270' were grouped among the best ones for various characteristics such as mass and total number of roots, marketable root mass, the first two showed a high specific weight and '1270' intense orange color, indicative of high levels of &#946;-carotene