A Distinct Genetic Cluster in Cultivated Chickpea as Revealed by Genome-wide Marker Discovery and Genotyping

The accurate description of plant biodiversity is of utmost importance to efficiently address efforts in conservation genetics and breeding. Herein, we report the successful application of a genotyping-by-sequencing (GBS) approach in chickpea ( L.), resulting in the characterization of a cultivated germplasm collection with 3187 high-quality single nucleotide polymorphism (SNP) markers. Genetic structure inference, principal component analysis, and hierarchical clustering all indicated the identification of a genetic cluster corresponding to black-seeded genotypes traditionally cultivated in Southern Italy. Remarkably, this cluster was clearly distinct at both genetic and phenotypic levels from germplasm groups reflecting commercial chickpea classification into and seed types. Fixation index estimates for individual polymorphisms pointed out loci and genomic regions that might be of significance for the diversification of agronomic and commercial traits. Overall, our findings provide information on genetic relationships within cultivated chickpea and highlight a gene pool of great interest for the scientific community and chickpea breeding, which is limited by the low genetic diversity available in the primary gene pool

An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS

Background: Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation - that would replace current unspecific, time-consuming and labour-intensive processing of large samples - and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported. Results: Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150 mg fresh weight, FW) and root exudate (20 ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors - carlactone and carlactonoic acid. In combination with the optimized UHPLC-MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species - sorghum, rice, pea and tomato. Conclusion: The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC-MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.</p

Synteny-Based Development of CAPS Markers Linked to the Sweet kernel LOCUS, Controlling Amygdalin Accumulation in Almond (Prunus dulcis (Mill.) D.A.Webb)

The bitterness and toxicity of wild-type seeds of Prunoideae is due to the cyanogenic glucoside amygdalin. In cultivated almond (Prunus dulcis (Mill.) D.A. Webb), a dominant mutation at the Sk locus prevents amygdalin accumulation and thus results in edible sweet kernels. Here, we exploited sequence similarity and synteny between the genomes of almond and peach (Prunus persica (L.) Batsch) to identify cleaved amplified polymorphic sequence (CAPS) molecular markers linked to the Sk locus. A segregant F1 population was used to map these markers on the Sk genomic region, together with Sk-linked simple sequence repeat (SSR) markers previously described. Molecular fingerprinting of a cultivar collection indicated the possibility to use CAPS polymorphisms identified in this study in breeding programs arising from different parental combinations. Overall, we highlight a set of codominant markers useful for early selection of sweet kernel genotypes, an aspect of primary importance in almond breeding. In addition, by showing collinearity between the physical map of peach and the genetic map of almond with respect to the Sk genomic region, we provide valuable information for further marker development and Sk positional cloning.This work was financed by the projects “Mejora Genética del Almendro” (MINECO-Spain, AGL2017-85042-R), “The molecular mechanisms to break flower bud dormancy in fruit trees” to RS-P within the Villum Young Investigator Program and by the VILLUM Research Center for Plant Plasticity-Denmark, and “Breeding stone fruit species assisted by molecular tools” (Fundación Séneca-Spain).Peer reviewe

Characterization of low-strigolactone germplasm in pea (Pisum sativum L.) resistant to crenate broomrape (Orobanche crenata Forsk.)

Crenate broomrape (Orobanche crenata Forsk.) is a devastating parasitic weed threatening the cultivation of legumes around the Mediterranean and in theMiddle East. So far, only moderate levels of resistance were reported to occur in pea (Pisum sativum L.) natural germplasm, and most commercial cultivars are prone to severe infestation. Here, we describe the selection of a pea line highly resistant to O. crenata, following the screening of local genetic resources. Time series observations show that delayed emergence of the parasite is an important parameter associated with broomrape resistance. High performance liquid chromatography connected to tandem mass spectrometry analysis and in vitro broomrape germination bioassays suggest that the resistance mechanism might involve the reduced secretion of strigolactones, plant hormones exuded by roots and acting as signaling molecules for the germination of parasitic weeds. Two years of replicated trials in noninfested fields indicate that the resistance is devoid of pleiotropic effects on yield, in contrast to pea experimental mutants impaired in strigolactone biosynthesis and, thus, is suitable for use in breeding programs.</p