Genetic Diversity, Phylogenetics and Molecular Systematics of Guizotia Cass. (Asteraceae)

The genus Guizotia belongs to the tribe Heliantheae in the family Asteraceae. It has been placed under different subtribes. The genus has its center of origin, distribution and genetic diversity in Ethiopia, where G. abyssinica (niger) has been domesticated. Amplified Fragment Length Polymorphism (AFLP), Random Amplified Polymorphic DNA (RAPD) and DNA sequencing were applied to study the genetic diversity, phylogenetics, and molecular systematics of this genus. A large number of niger populations, representing all regions in Ethiopia where this crop is grown, was investigated using AFLP and RAPD molecular marker techniques. The extent of genetic variation in niger is distributed throughout its growing regions, regardless of the extent and altitude of cultivation. Despite the fact that most of the variation was within populations, significant population differentiation was obtained (AMOVA; P < 0.001) in all guizotias. It is concluded that both G. abyssinica and its wild and/or weedy relatives have wide genetic bases that need to be conserved and utilized for the improvement of G. abyssinica. Further collection of niger germplasm and exploration and conservation of highly localized guizotias are recommended. Most of the diagnostic markers generated from AFLPs and RAPDs in this study were specific to G. arborescens and G. zavattarii. Phylogenetic analyses of the genus Guizotia were undertaken based on molecular sequence data from the internal transcribed spacers (ITS) and five chloroplast DNA regions. The analyses revealed a close phylogenetic relationship between G. abyssinica and G. scabra ssp. schimperi and support the previous suggestion that the latter is the progenitor of the former. According to this study, G. scabra ssp. scabra, G. scabra ssp. schimperi, and the Chelelu and Ketcha populations are best viewed at present as separate species within the genus Guizotia. Those perennial guizotias with highly localized geographic distribution appears to have evolved first during the evolutionary history of the genus. This study supports the placement of the genus Guizotia within the subtribe Milleriinae. It is suggested that the present species composition of Guizotia and the subtribal placement of the genus need to be redefined

Untapped Genetic Resources for Breeding Acidic Soil-Adapted Chickpea (Cicer arietinum L.) Cultivars

Globally, more than half of potentially arable land is acidic, and aluminum (Al) is the primary factor limiting plant growth and crop productivity on acidic soils worldwide. The development and utilization of Al-tolerant crops is a sustainable approach to enhancing crop production on acidic soils. For this purpose, screening available genetic resources under Al-stressed conditions is a crucial initial step. Hence, the present study aimed to evaluate the Al tolerance of 264 Ethiopian chickpea landraces under hydroponic conditions without Al (control) and with 120 mu M Al (Al treatment). Significant (p < 0.001) variations were detected among the genotypes for all studied traits under control (0 mu M Al) and 120 mu M Al concentration. The relative growth values for the 120 mu M Al/0 mu M Al ratio was also significant, indicating the presence of a considerable amount of genetic variation in Ethiopian chickpea landraces in terms of Al tolerance. Based on relative root growth (RRG) as an Al-tolerance parameter, the genotypes were grouped into five distinct (p < 0.001) classes. The highest RRG value (1.59) was obtained for genotype ETC_209008, followed by ETC_41184 and ETC_212589, while ETC_208995 had the lowest RRG value of 0.27. Of the total landraces screened, 35% had higher RRG values than the tolerant genotype ETC_WL_1_2016 used as a reference, indicating the presence of adequate genotypes capable of outperforming the reference genotype on acidic soils. The genotypes identified in the present study may serve as sources of novel alleles in genes regulating Al tolerance in chickpea that can be utilized in breeding programs to improve the crop's adaptation to acidic soils, thus contributing to smallholder farmers' increased nutritional and food security

Population Genetic Analysis of Lobelia rhynchopetalum Hemsl. (Campanulaceae) Using DNA Sequences from ITS and Eight Chloroplast DNA Regions

DNA sequence data from the internal transcribed spacer of nuclear ribosomal DNA and eight chloroplast DNA regions were used to investigate haplotypic variation and population genetic structure of the Afroalpine giant lobelia, Lobelia rhynchopetalum. The study was based on eight populations sampled from two mountain systems in Ethiopia. A total of 20 variable sites were obtained, which resulted in 13 unique haplotypes and an overall nucleotide diversity (ND) of 0.281 ± 0.15 and gene diversity (GD) of 0.85 ± 0.04. Analysis of molecular variance (AMOVA) revealed a highly significant variation (P < 0.001) among populations (FST), and phylogenetic analysis revealed that populations from the two mountain systems formed their own distinct clade with >90% bootstrap support. Each population should be regarded as a significant unit for conservation of this species. The primers designed for this study can be applied to any Lobelia and other closely related species for population genetics and phylogenetic studies

Assessment of genetic diversity in Ethiopian field pea (Pisum sativum L.) accessions with newly developed EST-SSR markers

Passport data of Pisum sativum ssp. sativum L. varieties from NordGen that were used for genetic diversity analyses. (DOC 28 kb

QTL mapping for domestication-related characteristics in field cress (Lepidium campestre)—a novel oil crop for the Subarctic region

Domestication of a new crop requires identification and improvement of desirable characteristics Field cress (Lepidium campestre) is being domesticated as a new oilseed crop, particularly for northern temperate regions.. In the present study, an F2 mapping population and its F3 progenies were used to identify quantitative trait loci (QTLs) for plant height (PH), number of stems per plant (NS), stem growth orientation (SO), flowering habit (FH), earliness (ER), seed yield per plant (SY), pod shattering resistance (SHR), and perenniality (PE). A highly significant correlation (p &lt; 0.001) was observed between several pairs of characteristics, including SY and ER (negative) or ER and PE (positive). The inclusive composite interval mapping approach was used for QTL mapping using 2330 single nucleotide polymorphism (SNP) markers mapped across the eight field cress linkage groups. Nine QTLs were identified with NS, PH, SO, and PE having 3, 3, 2, and 1 QTLs, explaining 21.3%, 29.5%, 3.8%, and 7.2% of the phenotypic variation, respectively. Candidate genes behind three of the QTLs and favorable marker alleles for different classes of each characteristic were identified. Following their validation through further study, the identified QTLs and associated favorable marker alleles can be used in marker-aided breeding to speed up the domestication of field cress

Analysis of Genetic Diversity of Fescue Populations from the Highlands of Bolivia Using EST-SSR Markers

In the highlands of Bolivia, native Festuca species are an important source of feed for animals due to their high tolerance to low temperatures and drought. Using simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs), the genetic diversity of 43 populations of Festuca species from Oruro, La Paz, Potosi and Cochabamba departments was evaluated for the purpose of providing information for effective conservation and breeding. In total, 64 alleles were detected across the 43 populations. SSR locus NFA 142 (with 12 alleles) had the highest number of detected alleles, while locus FES 13 (with eight alleles) had the highest polymorphism information content (PIC) at 0.55. Based on Nei’s genetic distance between populations, the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis revealed two major clusters, each consisting of populations from the four departments. However, the analysis of molecular variance (AMOVA) revealed that only 5% of the total variation separated these two groups, indicating low genetic differentiation between the populations. It was also found that there was a low but significant differentiation (0.08%) between the population groups of the four departments (p = 0.01). The newly developed EST-SSR markers are highly valuable for evaluating the genetic diversity of Bolivian fescues and other related species

Discovering candidate SNPs for resilience breeding of red clover

Red clover is a highly valuable crop for the ruminant industry in the temperate regions worldwide. It also provides multiple environmental services, such as contribution to increased soil fertility and reduced soil erosion. This study used 661 single nucleotide polymorphism (SNP) markers via targeted sequencing using seqSNP, to describe genetic diversity and population structure in 382 red clover accessions. The accessions were selected from NordGen representing red clover germplasm from Norway, Sweden, Finland and Denmark as well as from Lantmännen, a Swedish seed company. Each accession was represented by 10 individuals, which was sequenced as a pool. The mean Nei’s standard genetic distance between the accessions and genetic variation within accessions were 0.032 and 0.18, respectively. The majority of the accessions had negative Tajima’s D, suggesting that they contain significant proportions of rare alleles. A pairwise FST revealed high genetic similarity between the different cultivated types, while the wild populations were divergent. Unlike wild populations, which exhibited genetic differentiation, there was no clear differentiation among all cultivated types. A principal coordinate analysis revealed that the first principal coordinate, distinguished most of the wild populations from the cultivated types, in agreement with the results obtained using a discriminant analysis of principal components and cluster analysis. Accessions of wild populations and landraces collected from southern and central Scandinavia showed a higher genetic similarity to Lantmännen accessios. It is therefore possible to link the diversity of the environments where wild populations were collected to the genetic diversity of the cultivated and wild gene pools. Additionally, least absolute shrinkage and selection operator (LASSO) models revealed associations between variation in temperature and precipitation and SNPs within genes controlling stomatal opening. Temperature was also related to kinase proteins, which are known to regulate plant response to temperature stress. Furthermore, the variation between wild populations and cultivars was correlated with SNPs within genes regulating root development. Overall, this study comprehensively investigated Nordic European red clover germplasm, and the results provide forage breeders with valuable information for further selection and development of red clover cultivars

Understanding the Sorghum–Colletotrichum sublineola interactions for enhanced host resistance

Improving sorghum resistance is a sustainable method to reduce yield losses due to anthracnose, a devastating disease caused by Colletotrichum sublineola. Elucidating the molecular mechanisms of sorghum–C. sublineola interactions would help identify biomarkers for rapid and efficient identification of novel sources for host-plant resistance improvement, understanding the pathogen virulence, and facilitating resistance breeding. Despite concerted efforts to identify resistance sources, the knowledge about sorghum–anthracnose interactions remains scanty. Hence, in this review, we presented an overview of the current knowledge on the mechanisms of sorghum-C. sublineola molecular interactions, sources of resistance for sorghum breeding, quantitative trait loci (QTL), and major (R-) resistance gene sequences as well as defense-related genes associated with anthracnose resistance. We summarized current knowledge about C. sublineola populations and its virulence. Illustration of the sorghum-C. sublineola interaction model based on the current understanding is also provided. We highlighted the importance of genomic resources of both organisms for integrated omics research to unravel the key molecular components underpinning compatible and incompatible sorghum–anthracnose interactions. Furthermore, sorghum-breeding strategy employing rapid sorghum germplasm screening, systems biology, and molecular tools is presented

Phenotypic Variability, Heritability and Associations of Agronomic and Quality Traits in Cultivated Ethiopian Durum Wheat (Triticum turgidum L. ssp. Durum, Desf.)

Quality is an important aspect of durum wheat in the processing sector. Thus, recognizing the variability of quality and agronomic traits and their association is fundamental in designing plant breeding programs. This study aimed to assess the variability, heritability, genetic advance, and correlation of some agronomic and quality traits among 420 Ethiopian durum wheat genotypes and to identify the promising genotypes with distinct processing quality attributes to produce superior quality pasta. The field experiment was conducted at two locations (Sinana and Chefe Donsa) using an alpha lattice design with two replications. Analysis of variance, chi-square test, and Shannon-Weaver diversity index revealed the existence of highly significant (p < 0.001) variation among genotypes for all studied traits. The broad-sense heritability values were ranging from 46.2% (days to maturity) to 81% (thousand kernel weight) with the genetic advance as a percent of the mean ranging from 1.1% (days to maturity) to 21.2% (grain yield). The phenotypic correlation coefficients for all possible pairs of quantitative traits showed a significant (p < 0.05) association among most paired traits. The gluten content (GC) and grain protein content (GPC) were negatively correlated with grain yield and yield-related traits and positively associated with phenological traits, while yield and phenological traits correlated negatively. The frequency distributions of amber-colored and vitreous kernels, which are preferable characters of durum wheat in processing, were highly dominant in Ethiopian durum wheat genotypes. The identified top 5% genotypes, which have amber color and vitreous kernel with high GC and GPC content as well as sufficient grain yield, could be directly used by the processing sector and/or as donors of alleles in durum wheat breeding programs

Genetic Diversity of Arabica Coffee ( Coffea arabica

Coffea arabica L. (arabica coffee), the only tetraploid species in the genus Coffea, represents the majority of the world’s coffee production and has a significant contribution to Nicaragua’s economy. The present paper was conducted to determine the genetic diversity of arabica coffee in Nicaragua for its conservation and breeding values. Twenty-six populations that represent eight varieties in Nicaragua were investigated using simple sequence repeat (SSR) markers. A total of 24 alleles were obtained from the 12 loci investigated across 260 individual plants. The total Nei’s gene diversity (HT) and the within-population gene diversity (HS) were 0.35 and 0.29, respectively, which is comparable with that previously reported from other countries and regions. Among the varieties, the highest diversity was recorded in the variety Catimor. Analysis of variance (AMOVA) revealed that about 87% of the total genetic variation was found within populations and the remaining 13% differentiate the populations (FST=0.13; P<0.001). The variation among the varieties was also significant. The genetic variation in Nicaraguan coffee is significant enough to be used in the breeding programs, and most of this variation can be conserved through ex situ conservation of a low number of populations from each variety