Identification of quantitative trait loci controlling root and shoot traits associated with drought tolerance in a lentil (Lens culinaris Medik.) recombinant inbred line population

Drought is one of the major abiotic stresses limiting lentil productivity in rainfed production systems. Specific rooting patterns can be associated with drought avoidance mechanisms that can be used in lentil breeding programs. In all, 252 co-dominant and dominant markers were used for Quantitative Trait Loci (QTL) analysis on 132 lentil recombinant inbred lines based on greenhouse experiments for root and shoot traits during two seasons under progressive drought-stressed conditions. Eighteen QTLs controlling a total of 14 root and shoot traits were identified. A QTL-hotspot genomic region related to a number of root and shoot characteristics associated with drought tolerance such as dry root biomass, root surface area, lateral root number, dry shoot biomass and shoot length was identified. Interestingly, a QTL (QRSratioIX-2.30) related to root-shoot ratio, an important trait for drought avoidance, explaining the highest phenotypic variance of 27.6 and 28.9% for the two consecutive seasons, respectively, was detected. This QTL was closed to the co-dominant SNP marker TP6337 and also flanked by the two SNP TP518 and TP1280. An important QTL (QLRNIII-98.64) related to lateral root number was found close to TP3371 and flanked by TP5093 and TP6072 SNP markers. Also, a QTL (QSRLIV-61.63) associated with specific root length was identified close to TP1873 and flanked by F7XEM6b SRAP marker and TP1035 SNP marker. These two QTLs were detected in both seasons. Our results could be used for marker-assisted selection in lentil breeding programs targeting root and shoot characteristics conferring drought avoidance as an efficient alternative to slow and labor-intensive conventional breeding methods

Mycorrhiza-mediated disease resistance

Arbuscular mycorrhizal fungi (AMF) play an essential role as one of the primary mutualistic plant‐microbe symbioses. Oral presentation on mycorrhiza-mediated disease resistance

Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.)

Linkage map. This file contains the details of the linkage map. (XLSX 38 kb

Advanced Imaging for Quantitative Evaluation of Aphanomyces Root Rot Resistance in Lentil

Aphanomyces root rot (ARR) is a soil-borne disease that results in severe yield losses in lentil. The development of resistant cultivars is one of the key strategies to control this pathogen. However, the evaluation of disease severity is limited to visual scores that can be subjective. This study utilized image-based phenotyping approaches to evaluate Aphanomyces euteiches resistance in lentil genotypes in greenhouse (351 genotypes from lentil single plant/LSP derived collection and 191 genotypes from recombinant inbred lines/RIL using digital Red-Green-Blue/RGB and hyperspectral imaging) and field (173 RIL genotypes using unmanned aerial system-based multispectral imaging) conditions. Moderate to strong correlations were observed between RGB, multispectral, and hyperspectral derived features extracted from lentil shoots/roots and visual scores. In general, root features extracted from RGB imaging were found to be strongly associated with disease severity. With only three root traits, elastic net regression model was able to predict disease severity across and within multiple datasets (R2 = 0.45–0.73 and RMSE = 0.66–1.00). The selected features could represent visual disease scores. Moreover, we developed twelve normalized difference spectral indices (NDSIs) that were significantly correlated with disease scores: two NDSIs for lentil shoot section – computed from wavelengths of 1170, 1160, 1270, and 1280 nm (0.12 ≤ |r| ≤ 0.24, P < 0.05) and ten NDSIs for lentil root sections – computed from wavelengths in the range of 630–670, 700–840, and 1320–1530 nm (0.10 ≤ |r| ≤ 0.50, P < 0.05). Root-derived NDSIs were more accurate in predicting disease scores with an R2 of 0.54 (RMSE = 0.86), especially when the model was trained and tested on LSP accessions, compared to R2 of 0.25 (RMSE = 1.64) when LSP and RIL genotypes were used as train and test datasets, respectively. Importantly, NDSIs – computed from wavelengths of 700, 710, 730, and 790 nm – had strong positive correlations with disease scores (0.35 ≤r ≤ 0.50, P < 0.0001), which was confirmed in field phenotyping with similar correlations using vegetation index with red edge wavelength (normalized difference red edge, 0.36 ≤ |r| ≤ 0.57, P < 0.0001). The adopted image-based phenotyping approaches can help plant breeders to objectively quantify ARR resistance and reduce the subjectivity in selecting potential genotypes

Genetic Relationship in Cicer Sp. Expose Evidence for Geneflow between the Cultigen and Its Wild Progenitor

There is a debate concerning mono- or poly-phyletic origins of the Near Eastern crops. In parallel, some authors claim that domestication was not possible within the natural range of the wild progenitors due to wild alleles flow into the nascent crops. Here we address both, the mono- or poly-phyletic origins and the domestications within or without the natural range of the progenitor, debates in order to understand the relationship between domesticated chickpea (Cicer arietinum L.) and its wild progenitor (C. reticulatum Ladizinsky) with special emphasis on its domestication centre in southeastern Turkey. A set of 103 chickpea cultivars and landraces from the major growing regions alongside wild accessions (C. reticulatum, C. echinospermum P.H Davis and C. bijugum K.H. Rech) sampled across the natural distribution range in eastern Turkey were genotyped with 194 SNPs markers. The genetic affinities between and within the studied taxa were assessed. The analysis suggests a mono-phyletic origin of the cultigen, with several wild accession as likely members of the wild stock of the cultigen. Clear separation between the wild and domesticated germplasm was apparent, with negligible level of admixture. A single C. reticulatum accession shows morphological and allelic signatures of admixture, a likely result of introgression. No evidence of geneflow from the wild into domesticated germplasm was found. The traditional farming systems of southeaster Turkey are characterized by occurrence of sympatric wild progenitor-domesticated forms of chickpea (and likewise cereals and other grain legumes). Therefore, both the authentic crop landraces and the wild populations native to the area are a unique genetic resource. Our results grant support to the notion of domestication within the natural distribution range of the wild progenitor, suggesting that the Neolithic domesticators were fully capable of selecting the desired phenotypes even when facing rare wild-domesticated introgression events

Identification of Mendel's White Flower Character

BACKGROUND: The genetic regulation of flower color has been widely studied, notably as a character used by Mendel and his predecessors in the study of inheritance in pea. METHODOLOGY/PRINCIPAL FINDINGS: We used the genome sequence of model legumes, together with their known synteny to the pea genome to identify candidate genes for the A and A2 loci in pea. We then used a combination of genetic mapping, fast neutron mutant analysis, allelic diversity, transcript quantification and transient expression complementation studies to confirm the identity of the candidates. CONCLUSIONS/SIGNIFICANCE: We have identified the pea genes A and A2. A is the factor determining anthocyanin pigmentation in pea that was used by Gregor Mendel 150 years ago in his study of inheritance. The A gene encodes a bHLH transcription factor. The white flowered mutant allele most likely used by Mendel is a simple G to A transition in a splice donor site that leads to a mis-spliced mRNA with a premature stop codon, and we have identified a second rare mutant allele. The A2 gene encodes a WD40 protein that is part of an evolutionarily conserved regulatory complex

Multiple post-domestication origins of kabuli chickpea through allelic variation in a diversification-associated transcription factor

Chickpea (Cicer arietinum) is among the founder crops domesticated in the Fertile Crescent. One of two major forms of chickpea, the so-called kabuli type, has white flowers and light-colored seed coats, properties not known to exist in the wild progenitor. The origin of the kabuli form has been enigmatic. We genotyped a collection of wild and cultivated chickpea genotypes with 538 single nucleotide polymorphisms (SNPs) and examined patterns of molecular diversity relative to geographical sources and market types. In addition, we examined sequence and expression variation in candidate anthocyanin biosynthetic pathway genes. A reduction in genetic diversity and extensive genetic admixture distinguish cultivated chickpea from its wild progenitor species. Among germplasm, the kabuli form is polyphyletic. We identified a basic helix-loop-helix (bHLH) transcription factor at chickpea\u27s B locus that conditions flower and seed colors, orthologous to Mendel\u27s A gene of garden pea, whose loss of function is associated invariantly with the kabuli type of chickpea. From the polyphyletic distribution of the kabuli form in germplasm, an absence of nested variation within the bHLH gene and invariant association of loss of function of bHLH among the kabuli type, we conclude that the kabuli form arose multiple times during the phase of phenotypic diversification after initial domestication of cultivated chickpea

Understanding photothermal interactions will help expand production range and increase genetic diversity of lentil (Lens culinaris Medik.)

Lentil is a staple in many diets around the world and growing in popularity as a quick-cooking, nutritious, plant-based source of protein in the human diet. Lentil varieties are usually grown close to where they were bred. Future climate change scenarios will result in increased temperatures and shifts in lentil crop production areas, necessitating expanded breeding efforts. We show how we can use a daylength and temperature model to identify varieties most likely to succeed in these new environments, expand genetic diversity, and give plant breeders additional knowledge and tools to help mitigate these changes for lentil producers.This research was conducted as part of the ‘Application of Genomics to Innovation in the Lentil Economy (AGILE)' project funded by Genome Canada and managed by Genome Prairie. We are grateful for the matching financial support from the Saskatchewan Pulse Growers, Western Grains Research Foundation, the Government of Saskatchewan, and the University of Saskatchewan. We acknowledge the support from our international partners: University of Basilicata (UNIBAS) in Italy; Institute for Sustainable Agriculture (IAS) in Spain; Center for Agriculture Research in the Dry Areas (ICARDA) in Morocco, India and Bangladesh; Local Initiatives for Biodiversity, Research and Development (LI-BIRD) in Nepal; and United States Department of Agriculture (USDA CRIS Project 5348-21000-017-00D) in the USA, for conducting field experiments in their respective countries

Geographical gradient of the <em>eIF4E</em> alleles conferring resistance to potyviruses in pea (<em>Pisum</em>) germplasm

<div><p>Background</p><p>The eukaryotic translation initiation factor 4E was shown to be involved in resistance against several potyviruses in plants, including pea. We combined our knowledge of pea germplasm diversity with that of the <i>eIF4E</i> gene to identify novel genetic diversity.</p><p>Methodology/Principal findings</p><p>Germplasm of 2803 pea accessions was screened for <i>eIF4E</i> intron 3 length polymorphism, resulting in the detection of four <i>eIF4E^A-B-C-S</i> variants, whose distribution was geographically structured. The <i>eIF4E^A</i> variant conferring resistance to the P1 PSbMV pathotype was found in 53 accessions (1.9%), of which 15 were landraces from India, Afghanistan, Nepal, and 7 were from Ethiopia. A newly discovered variant, <i>eIF4E^B</i>, was present in 328 accessions (11.7%) from Ethiopia (29%), Afghanistan (23%), India (20%), Israel (25%) and China (39%). The <i>eIF4E^C</i> variant was detected in 91 accessions (3.2% of total) from India (20%), Afghanistan (33%), the Iberian Peninsula (22%) and the Balkans (9.3%). The <i>eIF4E^S</i> variant for susceptibility predominated as the wild type. Sequencing of 73 samples, identified 34 alleles at the whole gene, 26 at cDNA and 19 protein variants, respectively. Fifteen alleles were virologically tested and 9 alleles (<i>eIF4E^{A-1-2-3-4-5-6-7}</i>, <i>eIF4E^B-1</i>, <i>eIF4E^C-2</i>) conferred resistance to the P1 PSbMV pathotype.</p><p>Conclusions/Significance</p><p>This work identified novel <i>eIF4E</i> alleles within geographically structured pea germplasm and indicated their independent evolution from the susceptible <i>eIF4E^S1</i> allele. Despite high variation present in wild <i>Pisum</i> accessions, none of them possessed resistance alleles, supporting a hypothesis of distinct mode of evolution of resistance in wild as opposed to crop species. The Highlands of Central Asia, the northern regions of the Indian subcontinent, Eastern Africa and China were identified as important centers of pea diversity that correspond with the diversity of the pathogen. The series of alleles identified in this study provides the basis to study the co-evolution of potyviruses and the pea host.</p></div

From Mendel’s discovery on pea to today’s plant genetics and breeding

In 2015, we celebrated the 150th anniversary of the presentation of the seminal work of Gregor Johann Mendel. While Darwin’s theory of evolution was based on differential survival and differential reproductive success, Mendel’s theory of heredity relies on equality and stability throughout all stages of the life cycle. Darwin’s concepts were continuous variation and “soft” heredity; Mendel espoused discontinuous variation and “hard” heredity. Thus, the combination of Mendelian genetics with Darwin’s theory of natural selection was the process that resulted in the modern synthesis of evolutionary biology. Although biology, genetics, and genomics have been revolutionized in recent years, modern genetics will forever rely on simple principles founded on pea breeding using seven single gene characters. Purposeful use of mutants to study gene function is one of the essential tools of modern genetics. Today, over 100 plant species genomes have been sequenced. Mapping populations and their use in segregation of molecular markers and marker–trait association to map and isolate genes, were developed on the basis of Mendel's work. Genome-wide or genomic selection is a recent approach for the development of improved breeding lines. The analysis of complex traits has been enhanced by high-throughput phenotyping and developments in statistical and modeling methods for the analysis of phenotypic data. Introgression of novel alleles from landraces and wild relatives widens genetic diversity and improves traits; transgenic methodologies allow for the introduction of novel genes from diverse sources, and gene editing approaches offer possibilities to manipulate gene in a precise manner