Analysis of genetic diversity and population structure of oilseed crop noug (Guizotia abyssinica) accessions collected from Ethiopia.

BACKGROUND: Noug is an Ethiopian indigenous oilseed crop cultivated primarily for its oil and various economic importance. Evaluating the extent of genetic diversity within and among populations is one of the most important steps in breeding and conservation measures. Thus, this study aimed to uncover the extent of genetic diversity and population structure of noug accessions collected from different regions of Ethiopia using microsatellite markers. METHODS AND RESULTS: A total of 161 accessions from fourteen regions of Ethiopia, including some from Eritrea using 13 microsatellite markers were analyzed. All the 13 microsatellite markers were polymorphic and highly informative with a mean PIC value of 0.82. The analysis generated a total of 158 alleles with a mean of 12.15 per locus. The overall mean of Shannon information index and heterozygosity/gene diversity were 1.57 and 0.74, respectively suggesting the presence of higher genetic diversity across the collection regions. AMOVA revealed that 96.06% of the total genetic variation was attributed to within populations while only 3.94% was attributed to among populations. Likewise, the dendrogram clustering, PCoA, and the model-based population structure analysis didn't exactly corresponded the grouping of the genotypes according to their regions of origin. CONCLUSION: The microsatellites used in the present study are highly informative and could be targeted for developing markers for future marker-assisted breeding. Genotypes collected from Shewa, Wollo, Gojjam, Tigray, and B/G showed a higher genetic diversity and private alleles as compared to other populations. Hence, these areas can be considered as hotspots which could help for the identification of genotypes that can be used in breeding programs as well as for the implementation of further conservation programs.

Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress.

MAIN CONCLUSION: Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.

Significant progressive heterobeltiosis in banana crossbreeding.

BACKGROUND: Heterobeltiosis is the phenomenon when the hybrid's performance is superior to its best performing parent. Banana (Musa spp. AAA) breeding is a tedious, time-consuming process, taking up to two decades to develop a consumer acceptable hybrid. Exploiting heterobeltiosis in banana breeding will help to select breeding material with high complementarity, thus increasing banana breeding efficiency. The aim of this study was therefore to determine and document the level of heterobeltiosis of bunch weight and plant stature in the East African highland bananas, in order to identify potential parents that can be used to produce offspring with desired bunch weight and stature after a few crosses. RESULTS: This research found significant progressive heterobeltiosis in cross-bred 'Matooke' (highland cooking) banana hybrids, also known as NARITAs, when grown together across years with their parents and grandparents in Uganda. Most (all except 4) NARITAs exhibited positive heterobeltiosis for bunch weight, whereas slightly more than half of them had negative heterobeltiosis for stature. The secondary triploid NARITA 17 had the highest heterobeltiosis for bunch weight: 249% versus its 'Matooke' grandparent and 136% against its primary tetraploid parent. Broad sense heritability (across three cropping cycles) for yield potential and bunch weight were high (0.84 and 0.76 respectively), while that of plant stature was very low (0.0035). There was a positive significant correlation (P < 0.05) between grandparent heterobeltiosis for bunch weight and genetic distance between parents (r = 0.39, P = 0.036), bunch weight (r = 0.7, P < 0.001), plant stature (r = 0.38, P = 0.033) and yield potential (r = 0.59, P < 0.001). Grandparent heterobeltiosis for plant stature was significantly, but negatively, correlated to the genetic distance between parents (r = - 0.6, P < 0.001). CONCLUSIONS: Such significant heterobeltiosis exhibited for bunch weight is to our knowledge the largest among main food crops. Since bananas are vegetatively propagated, the effect of heterobeltiosis is easily fixed in the hybrids and will not be lost over time after the release and further commercialization of these hybrids.

Genetic diversity of avocado from the southern highlands of Tanzania as revealed by microsatellite markers.

BACKGROUND: Avocado is an important cash crop in Tanzania, however its genetic diversity is not thoroughly investigated. This study was undertaken to explore the genetic diversity of avocado in the southern highlands using microsatellite markers. A total of 226 local avocado trees originating from seeds were sampled in eight districts of the Mbeya, Njombe and Songwe regions. Each district was considered as a population. The diversity at 10 microsatellite loci was investigated. RESULTS: A total of 167 alleles were detected across the 10 loci with an average of 16.7 ± 1.3 alleles per locus. The average expected and observed heterozygosity were 0.84 ± 0.02 and 0.65 ± 0.04, respectively. All but two loci showed a significant deviation from the Hardy-Weinberg principle. Analysis of molecular variance showed that about 6% of the variation was partitioned among the eight geographic populations. Population FST pairwise comparisons revealed lack of genetic differentiation for the seven of 28 population pairs tested. The principal components analysis (PCA) and hierarchical cluster analysis showed a mixing of avocado trees from different districts. The model-based STRUCTURE subdivided the trees samples into four major genetic clusters. CONCLUSION: High diversity detected in the analysed avocado germplasm implies that this germplasm is a potentially valuable source of variable alleles that might be harnessed for genetic improvement of this crop in Tanzania. The mixing of avocado trees from different districts observed in the PCA and dendrogram points to strong gene flow among the avocado populations, which led to population admixture revealed in the STRUCTURE analysis. However, there is still significant differentiation among the tree populations from different districts that can be utilized in the avocado breeding program.

Genetic diversity and population structure analyses of Plectranthus edulis (Vatke) Agnew collections from diverse agro-ecologies in Ethiopia using newly developed EST-SSRs marker system.

BACKGROUND: Plectranthus edulis (Vatke) Agnew (locally known as Ethiopian dinich or Ethiopian potato) is one of the most economically important edible tuber crops indigenous to Ethiopia. Evaluating the extent of genetic diversity within and among populations is one of the first and most important steps in breeding and conservation measures. Hence, this study was aimed at evaluating the genetic diversity and population structure of this crop using collections from diverse agro-ecologies in Ethiopia. RESULTS: Twenty polymorphic expressed sequence tag based simple sequence repeat (EST-SSRs) markers were developed for P. edulis based on EST sequences of P. barbatus deposited in the GenBank. These markers were used for genetic diversity analyses of 287 individual plants representing 12 populations, and a total of 128 alleles were identified across the entire loci and populations. Different parameters were used to estimate the genetic diversity within populations; and gene diversity index (GD) ranged from 0.31 to 0.39 with overall mean of 0.35. Hierarchical analysis of molecular variance (AMOVA) showed significant but low population differentiation with only 3% of the total variation accounted for variation among populations. Likewise, cluster and STRUCTURE analyses did not group the populations into sharply distinct clusters, which could be attributed to historical and contemporary gene flow and the reproductive biology of the crop. CONCLUSIONS: These newly developed EST-SSR markers are highly polymorphic within P. edulis and hence are valuable genetic tools that can be used to evaluate the extent of genetic diversity and population structure of not only P. edulis but also various other species within the Lamiaceae family. Among the 12 populations studied, populations collected from Wenbera, Awi and Wolaita showed a higher genetic diversity as compared to other populations, and hence these areas can be considered as hot spots for in-situ conservation as well as for identification of genotypes that can be used in breeding programs.

Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop.

BACKGROUND: The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Arabidopsis genes are among the most characterized genes in the plant kingdom and, hence, comparative genomics of Lepidium-Arabidopsis would facilitate the identification of Lepidium candidate genes regulating various desirable traits. RESULTS: Homologues of 30 genes known to regulate vernalization, flowering time, pod shattering, oil content and quality in Arabidopsis were identified and partially characterized in Lepidium. Alignments of sequences representing field cress and two of its closely related perennial relatives: L. heterophyllum and L. hirtum revealed 243 polymorphic sites across the partial sequences of the 30 genes, of which 95 were within the predicted coding regions and 40 led to a change in amino acids of the target proteins. Within field cress, 34 polymorphic sites including nine non-synonymous substitutions were identified. The phylogenetic analysis of the data revealed that field cress is more closely related to L. heterophyllum than to L. hirtum. CONCLUSIONS: There is significant variation within and among Lepidium species within partial sequences of the 30 genes known to regulate traits targeted in the present study. The variation within these genes are potentially useful to speed-up the process of domesticating field cress as future oil crop. The phylogenetic relationship between the Lepidium species revealed in this study does not only shed some light on Lepidium genome evolution but also provides important information to develop efficient schemes for interspecific hybridization between different Lepidium species as part of the domestication efforts.

A transnational and holistic breeding approach is needed for sustainable wheat production in the Baltic Sea region.

The Baltic Sea is one of the largest brackish water bodies in the world. Eutrophication is a major concern in the Baltic Sea due to the leakage of nutrients to the sea with agriculture being the primary source. Wheat (Triticum aestivum L.) is the most widely grown crop in the countries surrounding the Baltic Sea and thus promoting sustainable agriculture practices for wheat cultivation will have a major impact on reducing pollution in the Baltic Sea. This approach requires identifying and addressing key challenges for sustainable wheat production in the region. Implementing new technologies for climate-friendly breeding and digital farming across all surrounding countries should promote sustainable intensification of agriculture in the region. In this review, we highlight major challenges for wheat cultivation in the Baltic Sea region and discuss various solutions integrating transnational collaboration for pre-breeding and technology sharing to accelerate development of low input wheat cultivars with improved host plant resistance to pathogen and enhanced adaptability to the changing climate.

Molecular markers associated with aluminium tolerance in Sorghum bicolor.

BACKGROUND: Sorghum (Sorghum bicolor, L. Moench) production in many agro-ecologies is constrained by a variety of stresses, including high levels of aluminium (Al) commonly found in acid soils. Therefore, for such soils, growing Al tolerant cultivars is imperative for high productivity. METHODS: In this study, molecular markers associated with Al tolerance were identified using a mapping population developed by crossing two contrasting genotypes for this trait. RESULTS: Four SSR (Xtxp34, Sb5_236, Sb6_34, and Sb6_342), one STS (CTG29_3b) and three ISSR (811_1400, 835_200 and 884_200) markers produced alleles that showed significant association with Al tolerance. CTG29_3b, 811_1400, Xtxp34 and Sb5_236 are located on chromosome 3 with the first two markers located close to AltSB , a locus that underlie the Al tolerance gene (SbMATE) implying that their association with Al tolerance is due to their linkage to this gene. Although CTG29_3b and 811_1400 are located closer to AltSB , Xtxp34 and Sb5_236 explained higher phenotypic variance of Al tolerance indices. Markers 835_200, 884_200, Sb6_34 and Sb6_342 are located on different chromosomes, which implies the presence of several genes involved in Al tolerance in addition to SbMATE in sorghum. CONCLUSION: These molecular markers have a high potential for use in breeding for Al tolerance in sorghum.

Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers.

BACKGROUND: Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia. RESULTS: We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations. Eleven polymorphic simple sequence repeat (SSR) markers were used. We observed a total of 53 alleles across the eleven loci and individuals. In total, 32 alleles were detected in the cultivated populations, whereas 49 alleles were detected in the wild populations. We found higher genetic diversity in wild populations than in the cultivated counterpart. This result implies the potential of wild korarima as a possible source for novel alleles contributing to the improvement of cultivated korarima. Analysis of molecular variance (AMOVA) showed significant but low differentiation between cultivated and wild korarima populations. Similarly, neighbour-joining and STRUCTURE analyses did not group cultivated and wild populations into two distinct clusters. The lack of clear differentiation between cultivated and wild populations could be explained by historical and contemporary gene flow between the two gene pools. CONCLUSION: The 11 SSR loci developed in this study could be employed to examine genetic diversity and population structure of korarima in other countries as well as other Aframomum species. From the five administrative zones considered in this study, the Bench-Magi and Sheka zone showed populations with high genetic diversity, and these populations could be used as a potential starting point for in-situ and ex-situ germplasm conservation and korarima improvement through breeding programs after proper agronomic evaluation.

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

BACKGROUND: Field pea (Pisum sativum L.) is among the prominent crops in the world as food and feed. There are relatively few simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) in P. sativum. RESULTS: In the present study, 15 new EST-SSR markers were developed from publicly available ESTs. These markers have successfully amplified their target loci across seven Pisum sativum subsp. sativum accessions. Eleven (73%) of these SSRs were trinucleotide repeats, two (13%) dinucleotide and two (13%) were hexanucleotide repeats. Across-taxa transferability of these new markers was also tested on other subspecies of Pisum as well as on P. fulvum, Vicia faba and Lens culinaris. In Pisum sativum subsp. sativum, 13 of the 15 markers were polymorphic and 12 of them subsequently used for genetic diversity analysis. Forty six accessions, of which 43 were from Ethiopia, were subjected to genetic diversity analysis using these newly developed markers. All accessions were represented by 12 individuals except two (NGB103816 and 237508) that were represented by 9 and 11 individuals, respectively. A total of 37 alleles were detected across all accessions. PS10 was the most polymorphic locus with six alleles, and the average number of alleles per locus over the 12 polymorphic loci was 3.1. Several rare and private alleles were also revealed. The most distinct accession (32048) had private alleles at three loci with 100% frequency. CONCLUSION: These newly developed EST-SSR primer-pairs successfully amplified expected loci in P. sativum subsp. sativum as well as in other subspecies of the genus Pisum and related genera. High levels of genetic variation were detected in field pea accessions from Ethiopia using these markers. This result implies the potential of the Ethiopian field pea gene pool for improvement of field peas in various desirable traits. In addition, these markers could be a valuable asset in resolving the inconsistency in the taxonomic status of the different subspecies of genus Pisum as well as for characterization of field pea accessions in different gene banks around the world for breeding and conservation purposes.

Modeling of Ethiopian Beef Meat Marbling Score Using Image Processing for Rapid Meat Grading.

Meat characterized by a high marbling value is typically anticipated to display enhanced sensory attributes. This study aimed to predict the marbling scores of rib-eye, steaks sourced from the Longissimus dorsi muscle of different cattle types, namely Boran, Senga, and Sheko, by employing digital image processing and machine-learning algorithms. Marbling was analyzed using digital image processing coupled with an extreme gradient boosting (GBoost) machine learning algorithm. Meat texture was assessed using a universal texture analyzer. Sensory characteristics of beef were evaluated through quantitative descriptive analysis with a trained panel of twenty. Using selected image features from digital image processing, the marbling score was predicted with R2 (prediction) = 0.83. Boran cattle had the highest fat content in sirloin and chuck cuts (12.68% and 12.40%, respectively), followed by Senga (11.59% and 11.56%) and Sheko (11.40% and 11.17%). Tenderness scores for sirloin and chuck cuts differed among the three breeds: Boran (7.06 ± 2.75 and 3.81 ± 2.24, respectively), Senga (5.54 ± 1.90 and 5.25 ± 2.47), and Sheko (5.43 ± 2.76 and 6.33 ± 2.28 Nmm). Sheko and Senga had similar sensory attributes. Marbling scores were higher in Boran (4.28 ± 1.43 and 3.68 ± 1.21) and Senga (2.88 ± 0.69 and 2.83 ± 0.98) compared to Sheko (2.73 ± 1.28 and 2.90 ± 1.52). The study achieved a remarkable milestone in developing a digital tool for predicting marbling scores of Ethiopian beef breeds. Furthermore, the relationship between quality attributes and beef marbling score has been verified. After further validation, the output of this research can be utilized in the meat industry and quality control authorities.

Durum wheat heat tolerance loci defined via a north-south gradient.

The global production of durum wheat (Triticum durum Desf.) is hindered by a constant rise in the frequency of severe heat stress events. To identify heat-tolerant germplasm, three different germplasm panels ("discovery," "investigation," and "validation") were studied under a range of heat-stressed conditions. Grain yield (GY) and its components were recorded at each site and a heat stress susceptibility index was calculated, confirming that each 1°C temperature rise corresponds to a GY reduction in durum wheat of 4.6%-6.3%. A total of 2552 polymorphic single nucleotide polymorphisms (SNPs) defined the diversity of the first panel, while 5642 SNPs were polymorphic in the "investigation panel." The use of genome-wide association studies revealed that 36 quantitative trait loci were associated with the target traits in the discovery panel, of which five were confirmed in a "subset" tested imposing heat stress by plastic tunnels, and in the investigation panel. A study of allelic combinations confirmed that Q.icd.Heat.003-1A, Q.icd.Heat.007-1B, and Q.icd.Heat.016-3B are additive in nature and the positive alleles at all three loci resulted in a 16% higher GY under heat stress. The underlying SNPs were converted into kompetitive allele specific PCR markers and tested on the validation panel, confirming that each explained up to 9% of the phenotypic variation for GY under heat stress. These markers can now be used for breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

Genetic Diversity of Durum Wheat (Triticum turgidum L. ssp. durum, Desf) Germplasm as Revealed by Morphological and SSR Markers.

Ethiopia is considered a center of origin and diversity for durum wheat and is endowed with many diverse landraces. This research aimed to estimate the extent and pattern of genetic diversity in Ethiopian durum wheat germplasm. Thus, 104 durum wheat genotypes representing thirteen populations, three regions, and four altitudinal classes were investigated for their genetic diversity, using 10 grain quality- and grain yield-related phenotypic traits and 14 simple sequence repeat (SSR) makers. The analysis of the phenotypic traits revealed a high mean Shannon diversity index (H' = 0.78) among the genotypes and indicated a high level of phenotypic variation. The principal component analysis (PCA) classified the genotypes into three groups. The SSR markers showed a high mean value of polymorphic information content (PIC = 0.50) and gene diversity (h = 0.56), and a moderate number of alleles per locus (Na = 4). Analysis of molecular variance (AMOVA) revealed a high level of variation within populations, regions, and altitudinal classes, accounting for 88%, 97%, and 97% of the total variation, respectively. Pairwise genetic differentiation and Nei's genetic distance analyses identified that the cultivars are distinct from the landrace populations. The distance-based (Discriminant Analysis of Principal Component (DAPC) and Minimum Spanning Network (MSN)) and model-based population stratification (STRUCTURE) methods of clustering grouped the genotypes into two clusters. Both the phenotypic data-based PCA and the molecular data-based DAPC and MSN analyses defined distinct groupings of cultivars and landraces. The phenotypic and molecular diversity analyses highlighted the high genetic variation in the Ethiopian durum wheat gene pool. The investigated SSRs showed significant associations with one or more target phenotypic traits. The markers identify landraces with high grain yield and quality traits. This study highlights the usefulness of Ethiopian landraces for cultivar development, contributing to food security in the region and beyond.

Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool.

Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.

Assigning Brassica microsatellite markers to the nine C-genome chromosomes using Brassica rapa var. trilocularis-B. oleracea var. alboglabra monosomic alien addition lines.

Brassica rapa var. trilocularis-B. oleracea var. alboglabra monosomic alien addition lines (MAALs) were used to assign simple sequence repeat (SSR) markers to the nine C-genome chromosomes. A total of 64 SSR markers specific to single C-chromosomes were identified. The number of specific markers for each chromosome varied from two (C3) to ten (C4, C7 and C9), where the designation of the chromosomes was according to Cheng et al. (Genome 38:313-319, 1995). Seventeen additional SSRs, which were duplicated on 2-5 C-chromosomes, were also identified. Using the SSR markers assigned to the previously developed eight MAALs and recently obtained aneuploid plants, a new Brassica rapa-B. oleracea var. alboglabra MAAL carrying the alien chromosome C7 was identified and developed. The application of reported genetically mapped SSR markers on the nine MAALs contributed to the determination of the correspondence between numerical C-genome cytological (Cheng et al. in Genome 38:313-319, 1995) and linkage group designations. This correspondence facilitates the integration of C-genome genetic information that has been generated based on the two designation systems and accordingly increases our knowledge about each chromosome. The present study is a significant contribution to genetic linkage analysis of SSR markers and important agronomic traits in B. oleracea and to the potential use of the MAALs in plant breeding.

Seed colour loci, homoeology and linkage groups of the C genome chromosomes revealed in Brassica rapa-B. oleracea monosomic alien addition lines.

BACKGROUND AND AIMS: Brassica rapa and B. oleracea are the progenitors of oilseed rape B. napus. The addition of each chromosome of B. oleracea to the chromosome complement of B. rapa results in a series of monosomic alien addition lines (MAALs). Analysis of MAALs determines which B. oleracea chromosomes carry genes controlling specific phenotypic traits, such as seed colour. Yellow-seeded oilseed rape is a desirable breeding goal both for food and livestock feed end-uses that relate to oil, protein and fibre contents. The aims of this study included developing a missing MAAL to complement an available series, for studies on seed colour control, chromosome homoeology and assignment of linkage groups to B. oleracea chromosomes. METHODS: A new batch of B. rapa-B. oleracea aneuploids was produced to generate the missing MAAL. Seed colour and other plant morphological features relevant to differentiation of MAALs were recorded. For chromosome characterization, Snow's carmine, fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH) were used. KEY RESULTS: The final MAAL was developed. Morphological traits that differentiated the MAALs comprised cotyledon number, leaf morphology, flower colour and seed colour. Seed colour was controlled by major genes on two B. oleracea chromosomes and minor genes on five other chromosomes of this species. Homoeologous pairing was largely between chromosomes with similar centromeric positions. FISH, GISH and a parallel microsatellite marker analysis defined the chromosomes in terms of their linkage groups. Conclusions A complete set of MAALs is now available for genetic, genomic, evolutionary and breeding perspectives. Defining chromosomes that carry specific genes, physical localization of DNA markers and access to established genetic linkage maps contribute to the integration of these approaches, manifested in the confirmed correspondence of linkage groups with specific chromosomes. Applications include marker-assisted selection and breeding for yellow seeds.

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 (F(ST)), 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.

Genetic diversity of arabica coffee (Coffea arabica L.) in Nicaragua as estimated by simple sequence repeat markers.

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 (H(T)) and the within-population gene diversity (H(S)) 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 (F(ST) = 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.

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.

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.