Jonathan Fresnedo-Ramírez

A next-generation marker genotyping platform (AmpSeq) in heterozygous crops: a case study for marker-assisted selection in grapevine

Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates trait-associated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and acylated anthocyanins) in grapevine breeding. The vast majority of sequence reads (⩾99%) were from the targeted regions. Across 380 individuals and up to 31 amplicons sequenced in each lane of MiSeq data, most amplicons (83 to 87%) had <10% missing data, and read depth had a median of 220–244×. Several strengths of the AmpSeq platform that make this approach of broad interest in diverse crop species include accuracy, flexibility, speed, high-throughput, low-cost and easily automated analysis.

Application of Genomic and Quantitative Genetic Tools to Identify Candidate Resistance Genes for Brown Rot Resistance in Peach

The availability of a complete peach genome assembly and three different peach genome sequences created by our group provide new opportunities for application of genomic data and can improve the power of the classical Quantitative Trait Loci (QTL) approaches to identify candidate genes for peach disease resistance. Brown rot caused by Monilinia spp., is the most important fungal disease of stone fruits worldwide. Improved levels of peach fruit rot resistance have been identified in some cultivars and advanced selections developed in the UC Davis and USDA breeding programs. Whole genome sequencing of the Pop-DF parents lead to discovery of high-quality SNP markers for QTL genome scanning in this experimental population. Pop-DF created by crossing a brown rot moderately resistant cultivar ‘Dr. Davis’ and a brown rot resistant introgression line, ‘F8,1–42’, derived from an initial almond × peach interspecific hybrid, was evaluated for brown rot resistance in fruit of harvest maturity over three seasons. Using the SNP linkage map of Pop-DF and phenotypic data collected with inoculated fruit, a genome scan for QTL identified several SNP markers associated with brown rot resistance. Two of these QTLs were placed on linkage group 1, covering a large (physical) region on chromosome 1. The genome scan for QTL and SNP effects predicted several candidate genes associated with disease resistance responses in other host-pathogen systems. Two potential candidate genes, ppa011763m and ppa026453m, may be the genes primarily responsible for M. fructicola recognition in peach, activating both PAMP-triggered immunity (PTI) and effector-triggered immunity (ETI) responses. Our results provide a foundation for further genetic dissection, marker assisted breeding for brown rot resistance, and development of peach cultivars resistant to brown rot.

Diversity and distribution of genus Jatropha in Mexico

In Mexico and all over the world, the number of studies on the species of the Jatropha genus has increased because of the use of its seed oil to produce biodiesel. However, the knowledge of the taxonomy, distribution, and ethnobotany of these and related species is incomplete. This article presents the distribution of the genus in Mexico according to its internationally accepted taxonomic identity. The distribution is linked to environmental variables such as elevation, climate type, soil, and soil moisture patterns. In addition to showing the current taxonomical knowledge in Mexico, this article discusses its biogeography, its traditional uses and the research lines to follow in further study of the genus. The distribution results show that some species are broadly adapted; as a consequence, they are present in many different environments. Species such as J. dioica, J. curcas, J. cordata, J. cinerea and J. gaumeri are distributed in areas with well defined environmental conditions. However, the distribution of species such as J. riojae has not yet been ascertained. Three areas with high species richness were identified, and they are very important for the study and conservation of the genus. Mexico is a global center of diversity for this genus. Food and medicinal uses have been reported for some species. This article concludes with recommendations for further study to improve the knowledge of this genus in Mexico.

Influence of year and genetic factors on chilling injury susceptibility in peach (Prunus persica (L.) Batsch)

Chilling injury (CI) is a major physiological problem limiting consumption and export of peach and nectarine (Prunus persica (L.) Batsch). To clarify the genetic basis for chilling injury, inheritance of the major CI symptoms mealiness, flesh browning, flesh bleeding, and flesh leatheriness were examined over three years in two related peach progenies. In addition, genetic relationships among traits and the year-to-year variation in trait performance in these progenies were tracked. Both populations also segregated for Freestone-Melting flesh (F-M) and yellow flesh. There were significant differences in CI symptoms among years. The major gene endoPG, which controls the F-M locus, provides resistance to mealiness in non-melting flesh fruit. Only fruit with melting flesh can develop mealiness if the tree possesses other genetic susceptibility factors and/or experiences inducing conditions. The F-M locus also greatly influences susceptibility to flesh bleeding, although the physiological mechanism for this disorder is unclear and may be controlled by a different gene closely linked to endoPG. Unlike mealiness, flesh bleeding occurred primarily in non-melting flesh fruit, particularly when the fruit is white-fleshed. Flesh browning incidence was greater in mealy fruit and was not associated with flesh bleeding. Breeding for CI resistance is thus a viable long-term strategy to reduce losses in the fresh and processed peach and nectarine industries. This study is an important first step to understanding genetic control of CI symptoms in peach.

Morphovariability of capulín (Prunus serotina Ehrh.) in the central-western region of Mexico from a plant genetic resources perspective

The capulín, or black cherry tree (Prunus serotina Ehrh.) is a tree with edible fruits native to North America that has been used not just as a source of food but also as a source of energy (its wood) since prehispanic times. Mexico has three of the five botanical subspecies in the P. serotina botanical complex, which have not yet been characterized for agricultural purposes. It is desirable to determine whether capulín trees comprise a homogeneous group or whether there are separate morpho-types. This study focuses on the morphological variability of seven populations from the western and central regions of Mexico. We used the Hill & Smith Analysis and graphical methods to analyze and interpret data with respect to 22 quantitative morphological characters and 17 qualitative morphological characters, all from different plant organs. Two major geographically and morphologically related groups were clearly identified, and the morphological variability in the study zone was related to taxonomic, genetic and agronomic factors. The results are discussed from a genetic resources perspective. The genetic, cultural, ecological and agronomic implications of these results are also considered, as well as the potential uses for the species. From these results, an agro-morphological characterization can be developed, in order to identify interesting types of capulín for fruit and seed production in agro-industry, or as rootstock for related species and forestry uses. Our results have implications for the conservation and sustainable use of capulín genetic resources in the central and western regions of Mexico.

Next Generation Mapping of Enological Traits in an F2 Interspecific Grapevine Hybrid Family.

In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F1 families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing (GBS) technology in an F2 mapping family of 424 progeny derived from a cross between the wild species V. riparia Michx. and the interspecific hybrid winegrape cultivar, ‘Seyval’. The resulting map has 1449 markers spanning 2424 cM in genetic length across 19 linkage groups, covering 95% of the genome with an average distance between markers of 1.67 cM. Compared to an SSR map previously developed for this F2 family, these results represent an improved map covering a greater portion of the genome with higher marker density. The accuracy of the map was validated using the well-studied trait berry color. QTL affecting YAN, MA and SS related traits were detected. A joint MA and SS QTL spans a region with candidate genes involved in the malate metabolism pathway. We present an analytical pipeline for calling intercross GBS markers and a high-density linkage map for a large F2 family of the highly heterozygous Vitis genus. This study serves as a model for further genetic investigations of the molecular basis of additional unique characters of North American hybrid wine cultivars and to enhance the breeding process by marker-assisted selection. The GBS protocols for identifying intercross markers developed in this study can be adapted for other heterozygous species.

Lessons from a Phenotyping Center Revealed by the Genome-Guided Mapping of Powdery Mildew Resistance Loci

The genomics era brought unprecedented opportunities for genetic analysis of host resistance, but it came with the challenge that accurate and reproducible phenotypes are needed so that genomic results appropriately reflect biology. Phenotyping host resistance by natural infection in the field can produce variable results due to the uncontrolled environment, uneven distribution and genetics of the pathogen, and developmentally regulated resistance among other factors. To address these challenges, we developed highly controlled, standardized methodologies for phenotyping powdery mildew resistance in the context of a phenotyping center, receiving samples of up to 140 grapevine progeny per F1 family. We applied these methodologies to F1 families segregating for REN1- or REN2-mediated resistance and validated that some but not all bioassays identified the REN1 or REN2 locus. A point-intercept method (hyphal transects) to quantify colony density objectively at 8 or 9 days postinoculation proved to be the phenotypic response most reproducibly predicted by these resistance loci. Quantitative trait locus (QTL) mapping with genotyping-by-sequencing maps defined the REN1 and REN2 loci at relatively high resolution. In the reference PN40024 genome under each QTL, nucleotide-binding site-leucine-rich repeat candidate resistance genes were identified-one gene for REN1 and two genes for REN2. The methods described here for centralized resistance phenotyping and high-resolution genetic mapping can inform strategies for breeding resistance to powdery mildews and other pathogens on diverse, highly heterozygous hosts.

The Floral Biology of Jatropha curcas L.—A Review

Jatropha curcas L. (Euphorbiaceae) has attracted considerable recent attention as a potential horticultural crop based on the quality of its oil seed for biodiesel production, and its ability to grow in unproductive subtropical or subdesert soils. Additionally, several characteristics of the species make it a good model for a more thorough understanding of the reproductive biology of a species undergoing the domestication process. To date, there is limited information about its reproductive patterns and the genetics involved. Such information is necessary for developing efficient agronomic practices and for guiding the research needed to more fully understand the species’ reproduction processes. J. curcas has an inconsistent mating system, which presents both opportunities and challenges in developing breeding strategies and agronomic practices. Unraveling the mating system of J. curcas can increase our understanding of the evolution of reproduction systems in monoecious plants. The influences of environmental factors on flowering and floral organ development have not been reported under either field or controlled conditions. Moreover, no genetic mechanisms controlling the characteristics of the flowering (architecture, sex expression and sex ratios) have been proposed. The present review assesses and synthesizes the current knowledge of the floral biology of J. curcas. It provides a description of the species, its reproductive organs and reproductive patterns, and discussing the factors influencing them.

Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs

Taraxacum kok-saghyz (TK) is a potential alternative crop for natural rubber (NR) production, due to its high molecular weight rubber, short breeding cycle, and diverse environmental adaptation. However, improvements in rubber yield and agronomically relevant traits are still required before it can become a commercially-viable crop. An RNA-Seq based transcriptome was developed from a pool of roots from genotypes with high and low rubber yield. A total of 55,532 transcripts with lengths over 200 bp were de novo assembled. As many as 472 transcripts were significantly homologous to 49 out of 50 known plant putative rubber biosynthesis related genes. 158 transcripts were significantly differentially expressed between high rubber and low rubber genotypes. 21,036 SNPs were different in high and low rubber TK genotypes. Among these, 50 SNPs were found within 39 transcripts highly homologous to 49 publically-searched rubber biosynthesis related genes. 117 SNPs were located within 36 of the differentially expressed gene sequences. This comprehensive TK transcriptomic reference, and large set of SNPs including putative exonic markers associated with rubber related gene homologues and differentially expressed genes, provides a solid foundation for further genetic dissection of rubber related traits, comparative genomics and marker-assisted selection for the breeding of TK.

Application of a Bayesian ordinal animal model for the estimation of breeding values for the resistance to Monilinia fruticola (G.Winter) Honey in progenies of peach [Prunus persica (L.) Batsch]

Fruit brown rot caused by Monilinia spp. is the most important fungal disease of stone fruits worldwide. Several phenotyping protocols to accurately characterize and evaluate brown rot infection have been proposed; however, the outcomes from those studies have not led to consistent advances in resistance breeding programs. Breeding for disease resistance is one of the most challenging objectives for crop improvement because disease expression is tetrahedral: it is simultaneously influenced by agent, host, environment, and human management. The present study presents a strategy based on Bayesian inference to analyze a peach breeding progeny for resistance to brown rot, evaluated using a polytomous ordinal scale. A pedigree containing two sources of resistance, one from peach and the other from almond, several commercial cultivars, and two segregating populations were analyzed to estimate the narrow-sense heritability (h2) and breeding values (EBVs) for brown rot resistance in progenies. Results show promise for genetic improvement of disease resistance and other traits characterized by strong environmental interactions.