Thawing the Frozen Shoulder

https://openriver.winona.edu/urc2018/1120/thumbnail.jp

Molecular, bioinformatic and statistical approaches to identify genes underlying complex traits in livestock

One of the primary goals for molecular geneticists working with livestock species is to identify and characterize genes underlying complex traits, the so-called quantitative trait loci (QTL). The primary strategy for identifying QTL involves several steps, one being fine mapping of a previously defined chromosomal region and another being identification of candidate genetic polymorphisms that may cause differences in phenotype. The studies presented in this dissertation address fine mapping methodology, use of the candidate gene approach for directly identifying candidate genetic polymorphisms and use of bioinformatic tools for identifying genetic polymorphisms in silico. Results from simulation studies suggest that two linkage disequilibrium-based fine mapping methods, one using haplotype information, the other using single marker information, provide QTL position estimates with comparable accuracy. Additional research is necessary to determine optimal fine mapping methods under experimental research conditions. The candidate gene studies presented, concerning the porcine connexin 37 (CX37) and bone morphogenetic factor 15 (BMP15) genes, highlight use of comparative sequence and biological information for identifying candidate genetic variants. Two synonymous mutations were discovered in the CX37 gene, which was subsequently mapped to SSC6 q24--31. However, these mutations were not significantly associated with fertility traits as hypothesized. Unfortunately, mutations could not be identified in BMP15, which was physically mapped to SSCX p11--13. Bioinformatic tools are shown here to be lucrative for identifying putative single nucleotide polymorphisms (SNPs) from redundant expressed sequence tag (EST) information in the pig. Using computer-derived SNPs, a correlation of 0.77 (p \u3c 0.00001) was found between the frequency of human and porcine SNPs in the coding regions (cSNPs) of 25 genes, while a correlation of 0.48 (p \u3c 0.0005) was found between the frequency of human and mouse cSNPs in 50 genes. This strong human-pig relationship should be verified in a larger sample so that SNP identification in pigs could be expedited by screening porcine genes homologous to human genes known to be SNP-dense in their coding regions. By capitalizing on statistical, bioinformatic and molecular tools in an integrated approach, the rate at which QTL are identified in livestock could be increased

Ethanol vapours limit Botrytis development over the postharvest life of table grapes

The application of ethanol vapours has been optimised over two seasons in order to prevent rot development, caused by Botrytis cinerea, and stem browning in 'Chasselas' table grapes. At a dose rate of 2 ml per kg of grapes, ethanol vapour was as effective as sulphur dioxide pads. Consumer panels detected no significant difference in sensory perception between controls and treated grapes. The ethanol vapour treatment could be easily implemented by the table grape industry since the technology is similar to sulphur dioxide treatment

Potential for Ethanol Vapours to Limit Table Grape Berry Shatter and to Limit Ethylene Evolution from Clusters

We have shown previously that ethanol vapours (given by 2 ml per kg of grapes) can prevent Botrytis development and stem browning, two of the major problems in postharvest quality of table grapes. In the present paper, we will give emphasis to preliminary results about (i) the role of ethanol vapours in the inhibition of berry shatter and (ii) the control of ethylene evolution from grapes bunches by ethanol vapours and the link to the control of Botryti

Development of an Organic Table Grape Production and Market in Switzerland

In Switzerland there is an increasing consumer demand for residue-free, organic table grapes. The organic cultivation of table grapes, however, is very delicate in humid climates and experience to advice organic growers is still lacking. The goal of our project that has started in 2004 is to develop and establish a cultivation system for organic table grapes under Swiss climatic and economic conditions with a high yield security and fulfilling the high quality demands of the market. Preliminary results: Interesting cultivars to produce are e.g. Fanny, Lilla, Palatina. However they are disease susceptible and must be produced under a rain roof. Better suited cultivars still need to be found. Consumer acceptance for organic table grapes produced in Switzerland is very positive. However changes towards new cultivars and lower production costs are necessary. Spray programs to achieve sufficient disease protection and no spray blotch seem to be realizable, mainly for production under rain roof

Patterns of genomic and phenomic diversity in wine and table grapes.

Grapes are one of the most economically and culturally important crops worldwide, and they have been bred for both winemaking and fresh consumption. Here we evaluate patterns of diversity across 33 phenotypes collected over a 17-year period from 580 table and wine grape accessions that belong to one of the world's largest grape gene banks, the grape germplasm collection of the United States Department of Agriculture. We find that phenological events throughout the growing season are correlated, and quantify the marked difference in size between table and wine grapes. By pairing publicly available historical phenotype data with genome-wide polymorphism data, we identify large effect loci controlling traits that have been targeted during domestication and breeding, including hermaphroditism, lighter skin pigmentation and muscat aroma. Breeding for larger berries in table grapes was traditionally concentrated in geographic regions where Islam predominates and alcohol was prohibited, whereas wine grapes retained the ancestral smaller size that is more desirable for winemaking in predominantly Christian regions. We uncover a novel locus with a suggestive association with berry size that harbors a signature of positive selection for larger berries. Our results suggest that religious rules concerning alcohol consumption have had a marked impact on patterns of phenomic and genomic diversity in grapes