Relationship of Cultivated Grain Amaranth Species and Wild Relative Accessions

Amaranthus is a genus of C4 dicotyledonous herbaceous plants, and three New World species have been domesticated to produce grain crops with light colored seed which are classified as pseudo-cereals rich in protein and minerals. A core collection of grain amaranths and immediate precursor species has been established, representing the closest related species. The goal of this study was to evaluate the genetic diversity in that collection of cultivated and wild species, using competitive allele single nucleotide polymorphism markers. A secondary objective was to determine the relationships among the three cultivated species and non-domesticated Amaranthus, while a third objective was to evaluate the utility of the markers in detecting diversity in the 276 genotypes. The markers were found to be highly variable with an average polymorphism information content of 0.365. All markers were bi-allelic; and the major allele frequency ranged from 0.388 to 0.871. Population structure analysis of the cultigens revealed the presence of two sub populations. Phylogeny confirmed that the two Mesoamerican species, Amaranthus cruentus and Amaranthus hypochondriacus, were related and distant from the South American species Amaranthus caudatus, which in turn was very closely clustered with Amaranthus quitensis, even though this is considered a weedy relative. The first pair of species were likely to have inter-crossed, while the latter two likely exist in a wild-cultivated hybrid state. In conclusion, the results of this SNP study provided insights on amaranth cultivars and their relationship to wild species, the probable domestication events leading to the cultivars, and possible crop breeding or germplasm conservation strategies

Diversity in Grain Amaranths and Relatives Distinguished by Genotyping by Sequencing (GBS)

The genotyping by sequencing (GBS) method has become a molecular marker technology of choice for many crop plants because of its simultaneous discovery and evaluation of a large number of single nucleotide polymorphisms (SNPs) and utility for germplasm characterization. Genome representation and complexity reduction are the basis for GBS fingerprinting and can vary by species based on genome size and other sequence characteristics. Grain amaranths are a set of three species that were domesticated in the New World to be high protein, pseudo-cereal grain crops. The goal of this research was to employ the GBS technique for diversity evaluation in grain amaranth accessions and close relatives from six Amaranthus species and determine genetic differences and similarities between groupings. A total of 10,668 SNPs were discovered in 94 amaranth accessions with ApeKI complexity reduction and 10X genome coverage Illumina sequencing. The majority of the SNPs were species specific with 4,568 and 3,082 for the two grain amaranths originating in Central America Amaranthus cruentus and A. hypochondriacus and 3,284 found amongst both A. caudatus, originally domesticated in South America, and its close relative, A. quitensis. The distance matrix based on shared alleles provided information on the close relationships of the two cultivated Central American species with each other and of the wild and cultivated South American species with each other, as distinguished from the outgroup with two wild species, A. powellii and A. retroflexus. The GBS data also distinguished admixture between each pair of species and the geographical origins and seed colors of the accessions. The SNPs we discovered here can be used for marker development for future amaranth study

Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed

Lessons from Common Bean on How Wild Relatives and Landraces Can Make Tropical Crops More Resistant to Climate Change

Warming is expected to lead to drier environments worldwide, especially in the tropics, and it is unclear how crops will react. Drought tolerance often varies at small spatial scales in natural ecosystems, where many of the wild relatives and landraces of the main crops have been collected. Through a series of examples, we will show that collections of wild relatives and landraces, many of those deposited at germplasm banks, may represent this desired source of variation, as they are genetically diverse and phenotypically variable. For instance, using a spectrum of genotyping and phenotyping approaches, we have studied the extent of genetic and phenotypic diversity for drought tolerance in wild and landraces of common bean (Phaseolus vulgaris L.) and compared it with the one available at cultivated varieties. Not surprisingly, most of the naturally available variation to cope with drought in the natural environments was lost through domestication and recent plant breeding. It is therefore imperative to exploit the reservoir of wild relatives and landraces to make crops more tolerant. Yet, it remains to be seen if the rate at which this naturally available variation can be incorporated into the cultivated varieties may keep pace with the rate of climate change

Naturally Available Genetic Adaptation in Common Bean and Its Response to Climate Change

Warming is expected to lead to drier environments worldwide, especially in the tropics, and it is unclear how crops will react. Drought tolerance often varies at small spatial scales in natural ecosystems, where many of the wild relatives and landraces of the main crops have been collected. Through a series of examples, we will show that collections of wild relatives and landraces, many of those deposited at germplasm banks, may represent this desired source of variation, as they are genetically diverse and phenotypically variable. For instance, using a spectrum of genotyping and phenotyping approaches, we have studied the extent of genetic and phenotypic diversity for drought tolerance in wild and landraces of common bean (Phaseolus vulgaris L.) and compared it with the one available at cultivated varieties. Not surprisingly, most of the naturally available variation to cope with drought in the natural environments was lost through domestication and recent plant breeding. It is therefore imperative to exploit the reservoir of wild relatives and landraces to make crops more tolerant. Yet, it remains to be seen if the rate at which this naturally available variation can be incorporated into the cultivated varieties may keep pace with the rate of climate change

Lab Fattening and Non-invasive Estimates of Body Composition in Deer Mice

Total body electrical conductivity measurements and lipid composition were determined for the deer mouse (Peromyscus maniculatus) to derive species specific calibration equations for use with EM-SCAN estimates of lean and fat tissue. For each individual, total body electrical conductivity was measured by EM-SCAN, and actual lipid content was determined by chemical extraction. Then, using estimated and actual lipid values, separate calibration equations were generated for freshly captured (lean) and laboratory maintained (fat) individuals, and a combined equation was derived for all individuals. These equations were variable in the accuracy of lipid estimates; the lowest relative error estimate (percent body fat) was obtained with the equation for fat individuals while the highest error (percent body fat) was associated with the lean condition. Although high average error rates for lipid might preclude the use of this approach when absolute accuracy is necessary with lean individuals, estimates of lean tissue were very accurate regardless of body composition condition. When removed from the field and maintained in the laboratory, body composition changed significantly and quite rapidly with relative body fat doubling in six weeks. Thus, maintenance under laboratory conditions might affect physiologic and behavioral parameters in such subjects

Development and diversity of Andean-derived, gene-based microsatellites for common bean (Phaseolus vulgaris L.)

<p>Abstract</p> <p>Background</p> <p>Gene-based (genic) microsatellites are a useful tool for plant genetics and simple sequence repeat loci can often be found in coding regions of the genome. While EST sequencing can be used to discover genic microsatellites, direct screening of cDNA libraries for repeat motifs can save on overall sequencing costs. The objective of this research was to screen a large cDNA library from and Andean common bean genotype for six di-nucleotide and tri-nucleotide repeat motifs through a filter hybridization approach and to develop microsatellite markers from positive clones.</p> <p>Results</p> <p>Robotics were used for high-throughput colony picking and to create a high-density filter of 18,432 double spotted cDNA clones which was followed by hybridization with repeat motif containing probes based on GA, CA, AAT, CAG, CAA and ACG repeats. A total of 1203 positive clones were identified by their addresses and sequenced from 5' ends and if required from 3' ends to confirm repeat motif and length. Out of 886 high quality sequences, 497 had complete microsatellite loci that were not truncated by the sequencing reaction and of these tri-nucleotide repeats were more common than di-nucleotide repeats. Different motifs were found in different frequencies in the 5' and 3' ends of the cDNAs. In a microsatellite development program, primers were designed for 248 SSR loci which were tested on a panel of 18 common bean genotypes to determine their potential as genetic markers finding higher average polymorphism information content for di-nucleotide repeat markers (0.3544) than for tri-nucleotide repeat markers (0.1536).</p> <p>Conclusion</p> <p>The present study provides a set of validated gene-based markers for common bean that are derived from G19833, an Andean landrace that is an important source of disease and abiotic stress tolerance which has been used for physical map development and as a mapping parent. Gene-based markers appear to be very efficient at separating divergent wild and cultivated accessions as well as Andean and Mesoamerican genepools and therefore will be useful for diversity analyses and for comparative and transcript mapping in common bean.</p

A Methyl Esterase 1 (PvMES1) Promotes the Salicylic Acid Pathway and Enhances Fusarium Wilt Resistance in Common Beans

Common bean (Phaseolus vulgaris L.) is an important food legume. Fusarium wilt caused by Fusarium oxysporum f. sp. phaseoli is one of the most serious soil-born diseases of common bean found throughout the world and affects the yield and quality of the crop. Few sources of Fusarium wilt resistance exist in legumes and most are of quantitative inheritance. In this study, we have identified a methyl salicylate esterase (MES), PvMES1, that contributes to plant defense response by regulating the salicylic acid (SA) mediated signaling pathway in response to Fusarium wilt in common beans. The result showed the role of PvMES1 in regulating SA levels in common bean and thus the SA signaling pathway and defense response mechanism in the plant. Overexpression of the PvMES1 gene enhanced Fusarium wilt resistance; while silencing of the gene caused susceptibility to the diseases. RNA-seq analysis with these transiently modified plants showed that genes related to SA level changes included the following gene ontologies: a) interaction between host and pathogen; b) phenylpropanoid synthesis; and c) sugar metabolism as well as others. These key signal elements activated the defense response pathway in common bean to Fusarium wilt. Collectively, our findings indicate that PvMES1 plays a pivotal role in regulating SA biosynthesis and signaling, and increasing Fusarium wilt resistance in common bean, thus providing novel insight into the practical applications of both SA and MES genes and pathways they contribiute to for developing elite crop varieties with enhanced broad-spectrum resistance to this critical disease