bims-plasge 2020-09-27 papers

Issue of 2020–09–27
four papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

J Appl Genet. 2020 Sep 23.

Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.).

Sandra Rychel-Bielska, Nelson Nazzicari, Piotr Plewiński, Wojciech Bielski, Paolo Annicchiarico, Michał Książkiewicz.

White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.

Keywords: Anthracnose resistance; Genomic selection; Marker-assisted selection; Quantitative trait; White lupin

DOI: https://doi.org/10.1007/s13353-020-00585-1

Plant Cell Rep. 2020 Sep 22.

Auxins, the hidden player in chloroplast development.

Alexis Salazar-Iribe, Clelia De-la-Peña.

Throughout decades of plant research, the plant hormones known as auxins have been found to be of vital importance in most plant development processes. Indole-3-acetic acid (IAA) represents the most common auxin in plants and can be synthesized from its tryptophan precursor, which is synthesized in the chloroplast. The chloroplast constitutes an organelle of great relevance to plants since the photosynthesis process by which plants get most of their energy is carried out there. The role of auxins in photosynthesis has been studied for at least 50 years, and in this time, it has been shown that auxins have an effect on several of the essential components and structure of the chloroplast. In recent decades, a high number of genes have been reported to be expressed in the chloroplast and some of their mutants have been shown to alter different auxin-mediated pathways. Genes in signaling pathways such as IAA/AUX, ARF, GH.3, SAUR and TIR, biosynthesis-related genes such as YUCCA and transport-related genes such as PIN have been identified among the most regulated genes in mutants related to alterations in the chloroplast. This review aims to provide a complete and updated summary of the relationship between auxins and several processes that involve the chloroplast, including chloroplast development, plant albinism, redox regulation and pigment synthesis.

Keywords: Albinism; Auxin; Chloroplast; Gene regulation; Photosynthesis; Tryptophan metabolism

DOI: https://doi.org/10.1007/s00299-020-02596-y

Mol Ecol. 2020 Sep 16.

Limited divergent adaptation despite a substantial environmental cline in wild pea.

Timo Hellwig, Shahal Abbo, Amir Sherman, Clarice Coyne, Yehoshua Saranga, Simcha Lev-Yadun, Doreen Main, Ping Zheng, Ron Ophir.

Isolation by environment (IBE) is a wide spread phenomenon in nature. It is commonly expected that the degree of differences among environments is proportional to the level of divergence between populations in the respective environments. Consequentially, it is assumed that species' genetic diversity displays pattern of IBE in the presence of a strong environmental cline if geneflow does not mitigate isolation. We tested this common assumption by analyzing the genetic diversity and demographic history of Pisum fulvum that inhabits contrasting habitats in the southern Levant and is expected to display only minor migration rates between populations, what makes it an ideal test case. Ecogeographic and subpopulation structure was analyzed and compared. Correlation of genetic with environmental distances was calculated to test the effect of IBD and IBE and detect the main drivers of these effects. Historic effective population size was estimated using stairwayplots. Limited overlap of ecogeographic and genetic clustering was observed, and correlation of genetic with environmental distances was statistically significant yet small. We detected a sharp decline of effective population size during the last glacial period. The low degree of IBE may be the result of genetic drift due to the past bottleneck. Our findings contradict the expectation that strong environmental clines cause IBE in the absence of extensive geneflow.

Keywords: demographic history; divergent adaptation; genetic diversity; isolation by distance; isolation by environment

DOI: https://doi.org/10.1111/mec.15633

Plant Dis. 2020 Sep 21. PDIS03200513RE

Partial Resistance Against Erysiphe pisi and E. trifolii Under Different Genetic Control in Lathyrus cicera: Outcomes from a Linkage Mapping Approach.

Carmen Santos, Davide Martins, Diego Rubiales, Maria Carlota Vaz Patto.

Powdery mildew infections are among the most severe foliar biotrophic fungal diseases in grain legumes. Several accessions of Lathyrus cicera (chickling pea) show levels of partial resistance to Erysiphe pisi, the causal agent of pea powdery mildew, and to E. trifolii, a powdery mildew pathogen recently confirmed to infect pea and Lathyrus spp. Nevertheless, the underlying L. cicera resistance mechanisms against powdery mildews are poorly understood. To unveil the genetic control of resistance against powdery mildews in L. cicera, a recombinant inbred line population segregating for response to both species was used in resistance linkage analysis. An improved L. cicera genetic linkage map was used in this analysis. The new higher-density linkage map contains 1,468 polymorphic loci mapped on seven major and two minor linkage groups, covering a total of 712.4 cM. The percentage of the leaf area affected by either E. pisi or E. trifolii was recorded in independent screenings of the recombinant inbred line population, identifying a continuous range of resistance-susceptibility responses. Distinct quantitative trait loci (QTLs) for partial resistance against each pathogen were identified, suggesting different genetic bases are involved in the response to E. pisi and E. trifolii in L. cicera. Moreover, through comparative mapping of L. cicera QTL regions with the pea reference genome, candidate genes and pathways involved in resistance against powdery mildews were identified. This study extended the previously available genetic and genomic tools in Lathyrus species, providing clues about diverse powdery mildew resistance mechanisms useful for future resistance breeding of L. cicera and related species.

Keywords: chickling pea; genetic linkage map; partial disease resistance; powdery mildew disease; quantitative trait loci; syntenic studies

DOI: https://doi.org/10.1094/PDIS-03-20-0513-RE