Informations et ressources scientifiques
sur le développement des zones arides et semi-arides

Titre : Improvements in semi-arid agriculture : Sorghum bicolor sub-population molecular marker development and mild salinity stress in Vitis

Auteur : Baggett, John Paul

Université de soutenance : University of Nevada Reno

Grade : Doctor of Philosophy (PhD) 2021

Résumé partiel
A multidisciplinary approach was taken to investigate two crops used in semi-aridagriculture (sorghum and grapevine). This dissertation is the result of two distinct projects. The first focused on sub-population specific molecular markers in sorghum and the second on salinity tolerance in grapevines. The work on sorghum tested the hypothesis : due to the genetic distinctions among sorghum sub-populations, molecular markers can be designed to differentiate and screen them in a high-throughput manner using next-generation sequencing. The work on grapevine tested the hypothesis : due to the previously reported correlation between photosynthetic decline and increased foliar Cl- concentrations in Vitis, foliar Cl- concentration increase is the cause of photosynthetic decline in Vitis. For the investigation of sub-population specific molecular marker development in sorghum, bioinformatic and plant breeding approaches were taken. For the investigation of grapevine salinity tolerance, plant physiology and bioinformatics techniques were employed. Recent plant breeding studies of several species have demonstrated the utility of combining molecular assessments of genetic distance with trait-linked SNP genotyping during the development of parent lines to maximize yield gains due to heterosis. SSRs (Short Sequence Repeat markers ; also known as microsatellite markers) are the molecular marker of choice to determine genetic diversity, but the methods historically used to sequence them have been burdensome. The ability to analyze SSRs in a higher-throughput manner independent of laboratory conditions would increase their utility in molecular ecology, germplasm curation, and plant breeding programs worldwide. This project reports simple bioinformatics methods that can be used to generate genome-wide de novo SSRs in silico followed by targeted Next Generation Sequencing (NGS) validation of those that provide the most information about sub-population identity of a breeding line, which influences heterotic group selection. While these methods were optimized in sorghum [Sorghum bicolor (L.) Moench], they were developed to be applied to any species with a reference genome and high-coverage whole-genome sequencing data of individuals from the sub-populations to be characterized.

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