Biology subjects

De Vega, J. J.

Publications and source records attributed to De Vega, J. J..

2 recordsLinked to original sources

bioRxiv2020

Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the crops clonal and polyploid nature and the pathogens rapid evolution. Genome-wide analysis (GWA) of multi-environment trials can add precision to breeding for complex traits. A diversity panel of tetraploid potato germplasm bread for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and phenotyped for late blight resistance in a trait observation network spanning three continents addressed by the International Potato Centers (CIPs) breeding program. The aims of this study were to (i) identify QTL underlying resistance in and across environments and (ii) develop prediction models to support the global deployment and use of promising resistance sources in local breeding and variety development programs. Health-indexed in vitro plants of 380 clones and varieties were distributed from CIP headquarters in Peru to China and Ethiopia and tuber seed was produced centrally in each country. Phenotypes were recorded as rAUDPC following field exposure to local isolates of Phytophthora infestans, Stringent filtering for individual read depth >60 resulted in 3,239 tetraploid SNPs. Meanwhile, 55,748 diploid SNPs were identified using diploidized data and individual read depth>17. The kinship matrix was utilized to obtain BLUP and identify best performing germplasm in each and all environments. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT and B3-LTVR populations. GWA identified stable QTL for late blight resistance in chromosome 9 and environment specific QTL in chromosomes 3, 5, 6 and 10.

genomics↗

bioRxiv2019

A new Brachiaria reference genome and its application in identifying genes associated with natural variation in tolerance to acidic soil conditions among Brachiaria grasses

Toxic concentrations of aluminium cations and low phosphorus availability are the main yield-limiting factors in acidic soils, which represent half of the potentially available arable land. Brachiaria grasses, which are commonly sown as a forage in the tropics because of their resilience and low demand for nutrients, have a greater tolerance to high concentrations of aluminium cations than most other grass crops. In this work, we explored the natural variation in tolerance to aluminium cations (Al3+) between high and low tolerant Brachiaria species and characterised their transcriptional differences during stress. We also identified three QTLs associated with root vigour during Al3+ stress in their hybrid progeny. By integrating these results with a new Brachiaria reference genome, we have identified 30 genes responsible for Al3+ tolerance in Brachiaria. We also observed differential expression during stress of genes involved in RNA translation, response signalling, cell wall composition and vesicle location genes homologous to aluminium-induced proteins involved in limiting uptake or localizing the toxin. However, there was limited regulation of malate transporters in Brachiaria, which are associated with external tolerance mechanisms to Al3+ stress in other grasses. The contrasting regulation of RNA translation and response signalling suggests response phasing is critical to Al3+ tolerance. HIGHLIGHTWe identified QTLs, genes and molecular responses in high and low tolerant Brachiaria grasses associated with aspects of response to aluminium stress, such as regulation, cell-wall composition and active transport.

genomics↗