Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe ‘‘domestication bottleneck’’ during pigeonpea domestication

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

Metabolomics-Driven Mining of Metabolite Resources:Applications and Prospects for Improving Vegetable Crops

Vegetable crops possess a prominent nutri-metabolite pool that not only contributes to the crop performance in the fields, but also offers nutritional security for humans. In the pursuit of identifying, quantifying and functionally characterizing the cellular metabolome pool, biomolecule separation technologies, data acquisition platforms, chemical libraries, bioinformatics tools, databases and visualization techniques have come to play significant role. High-throughput metabolomics unravels structurally diverse nutrition-rich metabolites and their entangled interactions in vegetable plants. It has helped to link identified phytometabolites with unique phenotypic traits, nutri-functional characters, defense mechanisms and crop productivity. In this study, we explore mining diverse metabolites, localizing cellular metabolic pathways, classifying functional biomolecules and establishing linkages between metabolic fluxes and genomic regulations, using comprehensive metabolomics deciphers of the plant’s performance in the environment. We discuss exemplary reports covering the implications of metabolomics, addressing metabolic changes in vegetable plants during crop domestication, stage-dependent growth, fruit development, nutri-metabolic capabilities, climatic impacts, plant-microbe-pest interactions and anthropogenic activities. Efforts leading to identify biomarker metabolites, candidate proteins and the genes responsible for plant health, defense mechanisms and nutri-rich crop produce are documented. With the insights on metabolite-QTL (mQTL) driven genetic architecture, molecular breeding in vegetable crops can be revolutionized for developing better nutritional capabilities, improved tolerance against diseases/pests and enhanced climate resilience in plants

Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

Pigeonpea (Cajanus cajan) is an annual or short-lived perennial food legume of acute regional importance, providing significant protein to the human diet in less developed regions of Asia and Africa. Due to its narrow genetic base, pigeonpea improvement is increasingly reliant on introgression of valuable traits from wild forms, a practice that would benefit from knowledge of its domestication history and relationships to wild species. Here we use 752 single nucleotide polymorphisms (SNPs) derived from 670 low copy orthologous genes to clarify the evolutionary history of pigeonpea (79 accessions) and its wild relatives (31 accessions). We identified three well-supported lineages that are geographically clustered and congruent with previous nuclear and plastid sequence-based phylogenies. Among all species analyzed Cajanus cajanifolius is the most probable progenitor of cultivated pigeonpea. Multiple lines of evidence suggest recent gene flow between cultivated and non-cultivated forms, as well as historical gene flow between diverged but sympatric species. Evidence supports that primary domestication occurred in India, with a second and more recent nested population bottleneck focused in tropical regions that is the likely consequence of pigeonpea breeding. We find abundant allelic variation and genetic diversity among the wild relatives, with the exception of wild species from Australia for which we report a third bottleneck unrelated to domestication within India. Domesticated C. cajan possess 75% less allelic diversity than the progenitor clade of wild Indian species, indicating a severe “domestication bottleneck” during pigeonpea domestication

Trichoderma asperellum T42 Reprograms Tobacco for Enhanced Nitrogen Utilization Efficiency and Plant Growth When Fed with N Nutrients

Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca2+ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO3- and NH4+ nutrients to tobacco at 40 and 70 days, particularly in NO3- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO3- nutrient confirming NO generation was dependent on NR pathway. NO3- dependent NO production contributed to increase in lateral root initiation, Ca2+ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO3- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO3-/NH4+ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO3-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil

Data_Sheet_1.docx

<p>Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca²⁺ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO₃^- and NH₄⁺ nutrients to tobacco at 40 and 70 days, particularly in NO₃^- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO₃^- nutrient confirming NO generation was dependent on NR pathway. NO₃^- dependent NO production contributed to increase in lateral root initiation, Ca²⁺ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO₃^- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO₃^-/NH₄⁺ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO₃^-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil.</p

Table_1.DOCX

<p>Trichoderma spp., are saprophytic fungi that can improve plant growth through increased nutrient acquisition and change in the root architecture. In the present study, we demonstrate that Trichoderma asperellum T42 mediate enhancement in host biomass, total nitrogen content, nitric oxide (NO) production and cytosolic Ca²⁺ accumulation in tobacco. T42 inoculation enhanced lateral root, root hair length, root hair density and root/shoot dry mass in tobacco under deprived nutrients condition. Interestingly, these growth attributes were further elevated in presence of T42 and supplementation of NO₃^- and NH₄⁺ nutrients to tobacco at 40 and 70 days, particularly in NO₃^- supplementation, whereas no significant increment was observed in nia30 mutant. In addition, NO production was more in tobacco roots in T42 inoculated plants fed with NO₃^- nutrient confirming NO generation was dependent on NR pathway. NO₃^- dependent NO production contributed to increase in lateral root initiation, Ca²⁺ accumulation and activities of nitrate transporters (NRTs) in tobacco. Higher activities of several NRT genes in response to T42 and N nutrients and suppression of ammonium transporter (AMT1) suggested that induction of high affinity NRTs help NO₃^- acquisition through roots of tobacco. Among the NRTs NRT2.1 and NRT2.2 were more up-regulated compared to the other NRTs. Addition of sodium nitroprusside (SNP), relative to those supplied with NO₃^-/NH₄⁺ nutrition and T42 treated plants singly, and with application of NO inhibitor, cPTIO, confirmed the altered NO fluorescence intensity in tobacco roots. Our findings suggest that T42 promoted plant growth significantly ant N content in the tobacco plants grown under N nutrients, notably higher in NO₃^-, providing insight of the strategy for not only tobacco but probably for other crops as well to adapt to fluctuating nitrate availability in soil.</p

Phylogeny of <i>Cajanus</i> species depicted as a 50% majority rule consensus tree.

<p>Tree topology was inferred with maximum parsimony via heuristic searches among 1000 trees. Numbers above branches indicate bootstrap support (>50%). The vertical bar indicates the putative projentitor species (two <i>C. Cajanifolius</i> accessions). Tree length  = 2145, consistency index (CI)  = 0.638, and retention index (RI)  = 0.837. The Bootstrap support for the sister relationship between wild-Australia and Wild-India clades (in the absence of the two <i>C. cajan</i> accessions) is 100% (data not shown).</p

Summary results of AMOVA analyses within and among populations of 95 accessions of the domesticated and wild groups.

<p>d.f.: Degrees of freedom; SS, sum of squared observations; MS, mean of squared observations; Est. var., estimated variance % Var., percentage of total variance; Fct, proportion of the total genetic variance between groups; FSc, proportion of the total genetic variance among populations within a group; Fst, proportion of the total genetic variance within populations.</p

Population structure of cultivated <i>Cajanus cajan</i>.

<p>Panel <b>A</b>, Weighted Neighbor-Joining tree depicting pairwise relationships between accessions. Colors denote the nature of individual accessions: Blue diamonds, cultivars and elite varieties; Pink diamonds, landraces; purple diamonds, ICRISAT reference material; Green diamonds, Core collection; Red diamonds, R-line; Orange diamonds, Minicore; Light green diamonds, Tropical; light blue, Indian; Light brown diamonds, Philipines. Genotypes with admixture between Indian and Tropical subgroups are designated by both light green and light blue diamonds. Panel <b>B</b>, population subdivisions with cultivated genotypes revealed by STRUCTURE. Green diamonds, genotypes with tropical distribution; blue diamonds, genotypes with an Indian sub-tropical distribution. Admixed genotypes are those with fractional membership in multiple groups. Likelihood values for each value of K are given in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0039563#pone.0039563.s004" target="_blank">Table S4</a>.</p