Genome‑wide association analyses of leaf rust resistance in cultivated emmer wheat

Leaf rust, caused by Puccinia triticina (Pt), constantly threatens durum (Triticum turgidum ssp. durum) and bread wheat (Triticum aestivum) production worldwide. A Pt race BBBQD detected in California in 2009 poses a potential threat to durum production in North America because resistance source to this race is rare in durum germplasm. To find new resistance sources, we assessed a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for seedling resistance to BBBQD and for adult resistance to a mixture of durum-specific races BBBQJ, CCMSS, and MCDSS in the field, and genotyped the panel using genotype-by-sequencing (GBS) and the 9 K SNP (Single Nucleotide Polymorphism) Infinium array. The results showed 24 and nine accessions consistently exhibited seedling and adult resistance, respectively, with two accessions providing resistance at both stages. We performed genome-wide association studies using 46,383 GBS and 4,331 9 K SNP markers and identified 15 quantitative trait loci (QTL) for seedling resistance located mostly on chromosomes 2B and 6B, and 11 QTL for adult resistance on 2B, 3B and 6A. Of these QTL, one might be associated with leaf rust resistance (Lr) gene Lr53, and two with the QTL previously reported in durum or hexaploid wheat. The remaining QTL are potentially associated with new Lr genes. Further linkage analysis and gene cloning are necessary to identify the causal genes underlying these QTL. The emmer accessions with high levels of resistance will be useful for developing mapping populations and adapted durum germplasm and varieties with resistance to the durum-specific races

Genomic and Transcriptomic Analyses of Nutrient Transporters in Plants

ABSTRACTGenomic and Transcriptomic Analyses of Nutrient Transporters in PlantsbyDhondup LhamoDoctor of Philosophy in Plant BiologyUniversity of California, BerkeleyProfessor Sheng Luan, Chair Plants require Nitrogen (N), phosphate (P), potassium (K) to support numerous physiological processes. These nutrients are acquired and transported by large families of nutrient transporters found in various tissues and cell types. Decades of research on nutrient channels and transporters in the model plant, Arabidopsis thaliana, have expanded our understanding of how these nutrients are transported, stored, remobilized, utilized and recycled within plants. However, our knowledge of the nutrient transport systems in crops are lacking. Whole-genome sequencing and transcriptomic analyses of diverse plant species are increasing exponentially each year, which can be utilized for comparative genomic analyses to understand the evolution of specific family of nutrient channels and transporters, their functional conservation and divergence at the sequence and tissue- and cell-type-specific levels. Camelina sativa is an emerging oilseed crop that contributes to food, feeds and fuels. It is considered to be tolerant to various harsh environments including low-nutrient stresses. However, it is not known how this polyploid might have evolved these adaptive traits at a gene level. To initiate functional genomic studies in this crop in response to low-nutrient stresses, we identified all the major nutrient channels/transporters of P and K present in the Camelina genome, and performed comprehensive and comparative genomic and transcriptomic analyses. We found that a whole-genome triplication event was the major driving force for the gene expansion, with three homoeologs for each Arabidopsis ortholog. In addition, tandem gene duplications have further expanded a specific nutrient transporter family in the Camelina genome. We also examined the phylogenetic relationship of nutrient transporters between Camelina and Arabidopsis, and analyzed their gene structures and protein domains to determine potential functional conservation and divergence at the sequence level. In silico RNA-seq analysis revealed potential candidate nutrient transporter genes that might function in specific tissue or organ for nutrient uptake, translocation and/or distribution. These studies represent the first effort in characterizing nutrient transporters in Camelina, and provide opportunities for future functional studies. The expression of nutrient transporter genes in specific cell, tissue and in response to various nutrient stresses are under the control of transcriptional factors (TFs). In Arabidopsis, AtSTOP1, a zinc finger TF is known to be involved in different abiotic stress response by modulating the transcript accumulation of different transporters. However, its involvement in low-K response have not been evaluated. Our study in Arabidopsis have revealed it is indeed involved, but the mechanism of its regulation is not understood. We isolated T-DNA insertion mutants of AtSTOP1 homolog in rice, named “Sensitive to K starvation 1” (sks1) based on its phenotype. RNA-seq analysis was performed in root and shoot tissues of wild type (WT) and sks1 mutants under low-K and the control conditions to understand its transcriptional program in low-K response. We identified a large number of genes to be mis-regulated in the mutants that are potentially involved in signal transduction, ROS production, immune response, cell wall synthesis, ion transport and homeostasis. Several low-K-inducible genes in WT such as TFs and signaling genes were controlled by SKS1 in roots, whereas many metabolic enzymes in shoots. We additionally found that SKS1 might be involved in signal integrations between nutrients, and between roots and shoots in response to low-K stress. While all these studies focus on gene expression of nutrient transporters and regulators at a tissue level, our understanding of the diverse transcriptional programs present in different cell types of a specific tissue is sparse. Recent advances in single-cell transcriptomics of Arabidopsis roots provided us with the opportunity to dissect the distribution of large sets of nutrient channels and transporters at a single cell resolution that work together to transfer nutrients from the soil to different cell-types of root cells and eventually reach vasculature for a massive flow. For this, we profiled the transcriptional patterns of putative nutrient transporters in different cell types of roots using the single-cell transcriptomics datasets from Arabidopsis root. Such analyses identified a number of NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow towards the vasculature. For long distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression pattern, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide a map of nutrient transport route from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future

Recent Advances in Genome-wide Analyses of Plant Potassium Transporter Families

Plants require potassium (K+) as a macronutrient to support numerous physiological processes. Understanding how this nutrient is transported, stored, and utilized within plants is crucial for breeding crops with high K+ use efficiency. As K+ is not metabolized, cross-membrane transport becomes a rate-limiting step for efficient distribution and utilization in plants. Several K+ transporter families, such as KUP/HAK/KT and KEA transporters and Shaker-like and TPK channels, play dominant roles in plant K+ transport processes. In this review, we provide a comprehensive contemporary overview of our knowledge about these K+ transporter families in angiosperms, with a major focus on the genome-wide identification of K+ transporter families, subcellular localization, spatial expression, function and regulation. We also expanded the genome-wide search for the K+ transporter genes and examined their tissue-specific expression in Camelina sativa, a polyploid oil-seed crop with a potential to adapt to marginal lands for biofuel purposes and contribution to sustainable agriculture. In addition, we present new insights and emphasis on the study of K+ transporters in polyploids in an effort to generate crops with high K+ Utilization Efficiency (KUE)

Genome-Wide Analysis of the Five Phosphate Transporter Families in Camelina sativa and Their Expressions in Response to Low-P

Phosphate transporters (PHTs) play pivotal roles in phosphate (Pi) acquisition from the soil and distribution throughout a plant. However, there is no comprehensive genomic analysis of the PHT families in Camelina sativa, an emerging oilseed crop. In this study, we identified 73 CsPHT members belonging to the five major PHT families. A whole-genome triplication event was the major driving force for CsPHT expansion, with three homoeologs for each Arabidopsis ortholog. In addition, tandem gene duplications on chromosome 11, 18 and 20 further enlarged the CsPHT1 family beyond the ploidy norm. Phylogenetic analysis showed clustering of the CsPHT1 and CsPHT4 family members into four distinct groups, while CsPHT3s and CsPHT5s were clustered into two distinct groups. Promoter analysis revealed widespread cis-elements for low-P response (P1BS) specifically in CsPHT1s, consistent with their function in Pi acquisition and translocation. In silico RNA-seq analysis revealed more ubiquitous expression of several CsPHT1 genes in various tissues, whereas CsPHT2s and CsPHT4s displayed preferential expression in leaves. While several CsPHT3s were expressed in germinating seeds, most CsPHT5s were expressed in floral and seed organs. Suneson, a popular Camelina variety, displayed better tolerance to low-P than another variety, CS-CROO, which could be attributed to the higher expression of several CsPHT1/3/4/5 family genes in shoots and roots. This study represents the first effort in characterizing CsPHT transporters in Camelina, a promising polyploid oilseed crop that is highly tolerant to abiotic stress and low-nutrient status, and may populate marginal soils for biofuel production

Plant Membrane Transport Research in the Post-genomic Era

Membrane transport processes are indispensable for many aspects of plant physiology including mineral nutrition, solute storage, cell metabolism, cell signaling, osmoregulation, cell growth, and stress responses. Completion of genome sequencing in diverse plant species and the development of multiple genomic tools have marked a new era in understanding plant membrane transport at the mechanistic level. Genes coding for a galaxy of pumps, channels, and carriers that facilitate various membrane transport processes have been identified while multiple approaches are developed to dissect the physiological roles as well as to define the transport capacities of these transport systems. Furthermore, signaling networks dictating the membrane transport processes are established to fully understand the regulatory mechanisms. Here, we review recent research progress in the discovery and characterization of the components in plant membrane transport that take advantage of plant genomic resources and other experimental tools. We also provide our perspectives for future studies in the field