The genetics of domestication of the azuki bean (Vigna angularis)

Genetic differences between azuki bean (Vigna angularis var. angularis) and its presumed wild ancestor (V. angularis var. nipponensis) were resolved into QTL for traits associated with adaptation to their respective distinct habits. A genetic linkage map constructed using progenies from a cross between Japanese cultivated and wild azuki beans covers 92.8% of the standard azuki bean linkage map. A reciprocal translocation between cultivated and wild azuki bean parents was identified on the basis of the linkage map having a pseudolinkage group and clustering of seed productivity-related QTL with large effect near the presumed breakpoints. In total, 162 QTL were identified for 46 domestication-related traits. Domestication of azuki bean has involved a trade-off between seed number and seed size: fewer but longer pods and fewer but larger seeds on plants with shorter stature in cultivated azuki bean being at the expense of overall seed yield. Genes found related to germination and flowering time in cultivated azuki bean may confer a selective advantage to the hybrid derivatives under some ecological conditions and may explain why azuki bean has evolved as a crop complex in Japan.     

The genetic diversity of the Vigna angularis complex in Asia.

A selected set of accessions of components of the azuki bean (Vigna angularis) complex comprising 123 cultivated accessions and 23 wild or weedy accessions from Bhutan, China (including Taiwan), India, Japan, Korea, and Nepal was analyzed using amplified fragment length polymorphism (AFLP) methodology. Using 12 AFLP primer pairs, 580 unambiguous bands were generated, 313 (53.9%) of which were polymorphic among azuki bean accessions. All 580 bands were used to assess phenotypic (band) and genetic (nucleotide) diversity among the 146 azuki bean accessions. The results indicate five major groups of azuki bean germplasm primarily associated with geographic origin of accessions and their status: wild, weedy, or cultivated. These five groups are (i) Himalayan wild, (ii) Nepal-Bhutan cultivated, (iii) Chinese wild, (iv) Taiwan wild - Bhutan cultivated, and (v) northeast Asian accessions. Within the northeast Asian accessions, three subgroups are present. These consist of (v1) Japanese complex - Korean cultivated, (v2) Japanese cultivated, and (v3) Chinese cultivated accessions. The results suggest domestication of azuki bean occurred at least twice, once in the Himalayan region of southern Asia and once in northeast Asia. The remarkable diversity of azuki bean germplasm in the Himalayan region compared with other regions suggests this is a rich source of germplasm for plant breeding. The results suggest there are important gaps in the germplasm collections of azuki bean and its close relatives from various parts of Asia and that specific collecting missions for Vigna germplasm related to azuki bean in the highlands of subtropical Asia are needed.     

Genetic diversity of the azuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) gene pool as assessed by SSR markers

To facilitate the wider use of genetic resources including newly collected cultivated and wild azuki bean germplasm, the genetic diversity of the azuki bean complex, based on 13 simple sequence repeat (SSR) primers, was evaluated and a core collection was developed using 616 accessions originating from 8 Asian countries. Wild germplasm from Japan was highly diverse and represented much of the allelic variation found in cultivated germplasm. The SSR results together with recent archaeobotanical evidence support the view that Japan is one center of domestication of azuki bean, at least for the northeast Asian azuki bean. Cultivated azuki beans from China, Korea, and Japan were the most diverse and were genetically distinct from each other, suggesting a long and relatively isolated history of cultivation in each country. Cultivated azuki beans from eastern Nepal and Bhutan were similar to each other and quite distinct from others. For two primers, most eastern Nepalese and Bhutanese cultivated accessions had null alleles. In addition, wild accessions from the Yangtze River region of China and the Himalayan region had a null allele for one or the other of these primers. Whether the distinct diversity of azuki bean in the Himalayan region is due to introgression or separate domestication events requires further study. In contrast, western Nepalese azuki beans showed an SSR profile similar to that of Chinese azuki beans. The genetic distinctness of cultivated azuki beans from Vietnam has been revealed for the first time. The specific alleles indicate that Vietnamese azuki beans have been cultivated in isolation from Chinese azuki beans for a long time. Wild germplasm from the Himalayan region showed the highest level of variation. Based on the results, Himalayan germplasm could be considered a novel gene source for azuki bean breeding. A comparison with mungbean SSR analysis revealed that the mean gene diversity of cultivated azuki bean (0.74) was much higher than that of cultivated mungbean (0.41). The reduction in gene diversity due to domestication, the domestication bottleneck, in azuki bean is not strong compared with that in mungbean.     

The development of SSR markers by a new method in plants and their application to gene flow studies in azuki bean [<Emphasis Type="Italic">Vigna angularis</Emphasis> (Willd.) Ohwi &; Ohashi]

To gain a better understanding of wild and weedy azuki population structures in relation to the cultigens we have developed simple sequence repeat (SSR) markers based on a new methodology for plant material. In the azuki bean genome, the number of (AG)_n and (AC)_n motif loci per haploid genome has been estimated to be 3,500 and 2,100, respectively, indicating that (AG)_n motifs are a rich source of markers. We constructed a (AG)_n-SSR-enriched library in azuki bean in order to obtain a comprehensive range of SSR markers efficiently. The method applied in this study resulted in a 116-fold enrichment over the non-enriched genomic library, with a high percentage (98%) of successful single-locus amplification by the primer pairs designed. Consequently, this method can be applied to construct SSR-enriched libraries suitable for large-scale sequencing. We obtained 255 unique sequences from an (AG)_n-enriched library for azuki bean. Fifty primer pairs were designed and screened against five populations of wild azuki bean. Among these five populations, one population from Bato town, Tochigi prefecture, Japan, showed greater polymorphism using these primers than the others and was therefore chosen for the in-depth study. The genotypes of 20 individuals were investigated using eight of the SSR primers developed. The genetic relationships among individuals revealed a complex spatial pattern of population structure. Although azuki bean is considered to be a predominantly self-pollinating species, 3 of the 20 individuals tested in the population showed heterozygous genotypes, indicating outcrossing. Allele size and DNA sequence in each of the 20 individuals were compared with those of landraces and released cultivars of azuki bean. Plants in part of the population had many alleles of the same size and with the same sequence as those in cultivated azuki bean, suggesting that gene flow from the cultigen to wild plants has occurred in this population. Unintentional transgene escape from azuki could therefore occur when transgenic azuki is grown in areas where its wild and weedy relatives occur. The approach used here could be applied to biosafety monitoring of transgenic azuki bean.Communicated by C. MöllersX.W. Wang and A. Kaga contributed equally to the results presented in this paper.     

Characterization of resistance to three bruchid species (Callosobruchus spp., Coleoptera,Bruchidae) in cultivated rice bean (Vigna umbellata)

Resistance of wild and cultivated rice bean (Vigna umbellata [Thunberg] Ohwi and Ohashi) to three bruchid species, Callosobruchus chinensis L., Callosobruchus maculatus F., and Callosobruchus analis F., was evaluated. All but three accessions of cultivated, and all wild rice bean accessions tested, exhibited complete resistance to all three bruchid species. Rice bean seeds with seed coat removed also showed complete resistance to the three bruchid species. Results indicate that physical attributes and/or chemical(s) present in the seed coat of rice bean are not the main factors responsible for resistance. Feeding tests were performed by using artificial beans prepared with varying proportions of rice bean (resistant) and azuki bean (susceptible) flour. Number of bruchid adults that emerged decreased, and larval developmental period (days) was extended, when artificial beans with an increasing proportion of rice bean flour were used. These tests revealed that a chemical compound(s) contained in the cotyledon of rice bean has an inhibitory effect on the growth of these bruchid species. The results also indicate that the chemical(s) in rice bean cotyledon is most effective against C. maculatus.     

The genetics of domestication of rice bean, Vigna umbellata

Background and Aims

The Asian genus Vigna, to which four cultivated species (rice bean, azuki bean, mung bean and black gram) belong, is suitable for comparative genomics. The aims were to construct a genetic linkage map of rice bean, to identify the genomic regions associated with domestication in rice bean, and to compare these regions with those in azuki bean.

Methods

A genetic linkage map was constructed by using simple sequence repeat and amplified fragment length polymorphism markers in the BC₁F₁ population derived from a cross between cultivated and wild rice bean. Using this map, 31 domestication-related traits were dissected into quantitative trait loci (QTLs). The genetic linkage map and QTLs of rice bean were compared with those of azuki bean.

Key Results

A total of 326 markers converged into 11 linkage groups (LGs), corresponding to the haploid number of rice bean chromosomes. The domestication-related traits in rice bean associated with a few major QTLs distributed as clusters on LGs 2, 4 and 7. A high level of co-linearity in marker order between the rice bean and azuki bean linkage maps was observed. Major QTLs in rice bean were found on LG4, whereas major QTLs in azuki bean were found on LG9.

Conclusions

This is the first report of a genetic linkage map and QTLs for domestication-related traits in rice bean. The inheritance of domestication-related traits was so simple that a few major QTLs explained the phenotypic variation between cultivated and wild rice bean. The high level of genomic synteny between rice bean and azuki bean facilitates QTL comparison between species. These results provide a genetic foundation for improvement of rice bean; interchange of major QTLs between rice bean and azuki bean might be useful for broadening the genetic variation of both species.     

Genome dissection of traits related to domestication in azuki bean (Vigna angularis) and comparison with other warm-season legumes

BACKGROUND: The objective of this study was to dissect into quantitative trait loci (QTLs) the large morphological and physiological differences between cultivated azuki bean (Vigna angularis) and a wild relative and to infer the commonalities of the QTLs for domestication-related traits across the Asian Vigna and with other warm-season legumes. METHODS: Two linkage maps, for the BC(1)F(1) and F(2) populations, respectively, from the same cross between azuki bean and V. nepalensis were developed. Using these linkage maps QTLs for 33 domestication-related traits were analysed and mapped. The location of mapped QTLs was compared with locations of similar QTLs in other warm-season legumes. KEY RESULTS: QTLs were detected for seed-, pod-, stem- and leaf-related traits. Most traits were controlled by between two and nine QTLs but several traits, such as pod dehiscence, were controlled by single genes. QTLs for domestication-related traits were restricted to particular regions of the azuki bean genome, especially linkage groups 1, 2, 4, 7 and 9. Linkage groups 1 and 2 had QTLs for a suite of traits including pod size, germination, seed size and lower stem length. QTLs on linkage groups 7 and 9 were associated with upper stem length, maximum leaf size and pod and seed size. Pleiotropy or close linkage of genes for domestication-related traits is suggested in these regions. While some QTLs are common to azuki bean and other warm-season legumes, many are recorded for the first time in azuki bean. CONCLUSIONS: QTLs for a large number of domestication-related traits have been mapped for the first time in azuki bean. QTLs with unexpected effect and new QTLs for traits such as seed size have been found. The results provide a foundation that will be useful for improvement of azuki bean and related legumes.     

Wild and Weed Azuki Beans in Japan

Wild azuki bean, a progenitor of an Asiatic food legume (Vigna angularis var.nipponensis: Fabaceae), and its weed form are distributed widely in the Japanese Archipelago. The straggling or climbing wildform occurs in sleeve or mantle plant communities, and the weakly climbing or bushy weed form is found in relatively open human-disturbed habitats. The wild form has small seeds with a black-mottled pattern on green or grey skin; the weed form has larger seeds with variable color patterns. Wild and weed forms have black, easily dehiscent pods, distinct from their cultivated counterpart which has red large seeds and indehiscent light-colored pods. The wild form is not utilized, but the weed form is recognized by farmers and has several folk names as a weed, a contaminated form of azuki bean, and a substitute for azuki as a food. The frequent occurrence of weed azuki bean in Japan is attributable to adaptation of the wildform to lack of climbing support in human-disturbed habitats, escape from old cultivars, and natural establishment from the derivatives of hybrids between cultivars and wild forms.     

Assessment of the importance of α-amylase inhibitor-2 in bruchid resistance of wild common bean

Both α-amylase inhibitor-2 (αAI-2) and arcelin have been implicated in resistance of wild common bean (Phaseolus vulgaris L.) to the Mexican bean weevil (Zabrotes subfasciatus Boheman). Near isogenic lines (NILs) for arcelin 1–5 were generated by backcrossing wild common bean accessions with a cultivated variety. Whereas seeds of a wild accession (G12953) containing both αAI-2 and arcelin 4 were completely resistant to Z. subfasciatus, those of the corresponding NIL were susceptible to infestation, suggesting that the principal determinant of resistance was lost during backcrossing. Three independent lines of transgenic azuki bean [Vigna angularis (Willd.) Ohwi and Ohashi] expressing αAI-2 accumulated high levels of this protein in seeds. The expression of αAI-2 in these lines conferred protection against the azuki bean weevil (Callosobruchus chinensis L.), likely through inhibition of larval digestive α-amylase. However, although the seed content of αAI-2 in these transgenic lines was similar to that in a wild accession of common bean (G12953), it did not confer a level of resistance to Z. subfasciatus similar to that of the wild accession. These results suggest that αAI-2 alone does not provide a high level of resistance to Z. subfasciatus. However, αAI-2 is an effective insecticidal protein with a spectrum of activity distinct from that of αAI-1, and it may prove beneficial in genetic engineering of insect resistance in legumes.     

野生小豆种质资源植株形态性状多样性分析

对来自中国、日本、韩国、缅甸4国的55份野生型、40份半野生型小豆种质资源植株形态性状的多样性进行分析,结果表明,野生型小豆与半野生型小豆在株高、平均成熟期、子粒颜色、百粒重等性状方面有明显的差别。95份小豆种质资源通过聚类分析,截值为1.488时可划分为5大类群。来源于缅甸和中国的野生型小豆种质各聚为1个类群,韩国和日本的种质混聚为3个类群。缅甸种质具平均成熟期长、茎秆粗、主茎分枝数多、百粒重轻等特点。中国贵州野生型种质植株较高、茎秆较细、单荚粒数较多、平均成熟期较长。日本野生型种质具有丰产特征。日本和韩国的半野生型小豆,平均成熟期较其他类群早、百粒重高、明度指数高。     

Phaseolin variability among wild and cultivated common beans (Phaseolus vulgaris) from Colombia

Phaseolin seed protein variability in a group of 8 wild and 77 cultivated common bean (Phaseolus vulgaris) accessions was determined using 1-dimensional SDS/ PAGE and 2-dimensional IEF-SDS/PAGE. Wild common bean accessions exhibited the 'CH' and 'B' patterns, previously undescribed among either wild or cultivated common beans. The cultivated genotypes showed (in decreasing frequency) the previously described 'S,' T,' and 'C phaseolin patterns as well as the new 'B' pattern similar to the pattern identified in a Colombian wild common bean accession. In the northeastern part of the Colombian bean-growing region, the cultivars exhibited almost exclusively an 'S' phaseolin type, while in the south-western part, the 'T' and 'C phaseolin cultivars were more frequent. Seed size analysis indicated that 'T' and 'C' phaseolin cultivars had larger seeds than 'S' and 'B' phaseolin cultivars. Our results suggest that Colombia is a meeting place for Andean and Middle American common bean germplasms, as well as a domestication center for the common bean.     

Sequence polymorphisms in wild,weedy, and cultivated rice suggest seed‐shattering locus sh4 played a minor role in Asian rice domestication

The predominant view regarding Asian rice domestication is that the initial origin of nonshattering involved a single gene of large effect, specifically, the sh4 locus via the evolutionary replacement of a dominant allele for shattering with a recessive allele for reduced shattering. Data have accumulated to challenge this hypothesis. Specifically, a few studies have reported occasional seed‐shattering plants from populations of the wild progenitor of cultivated rice (Oryza rufipogon complex) being homozygous for the putative “nonshattering” sh4 alleles. We tested the sh4 hypothesis for the domestication of cultivated rice by obtaining genotypes and phenotypes for a diverse set of samples of wild, weedy, and cultivated rice accessions. The cultivars were fixed for the putative “nonshattering” allele and nonshattering phenotype, but wild rice accessions are highly polymorphic for the putative “nonshattering” allele (frequency ~26%) with shattering phenotype. All weedy rice accessions are the “nonshattering” genotype at the sh4 locus but with shattering phenotype. These data challenge the widely accepted hypothesis that a single nucleotide mutation (“G”/“T”) of the sh4 locus is the major driving force for rice domestication. Instead, we hypothesize that unidentified shattering loci are responsible for the initial domestication of cultivated rice through reduced seed shattering.     

Genetic diversity of the Bambara groundnut (Vigna subterranea (L.) Verdc.) as assessed by SSR markers

Bambara groundnut ( Vigna subterranea (L.) Verdc.) is an important African legume crop. In this study, a collection consisting of 240 accessions was analyzed using 22 simple sequence repeat (SSR) markers. In total, 166 alleles were detected, with a mean of 7.59 alleles per locus. Allelic and gene diversities were higher in the west African and Cameroon/Nigeria regions with 6.68 and 6.18 alleles per locus, and 0.601 and 0.571, respectively. The genetic distance showed high similarity between west African and Cameroon/Nigeria accessions. Principal coordinate analyses and neighbor-joining analysis consistently revealed that the majority of west African accessions were grouped with Cameroon/Nigeria accessions, but they were differentiated from east African, central African, and southeast Asian accessions. Population structure analysis showed that two subpopulations existed, and most of the east African accessions were restricted to one subpopulation with some Cameroon/Nigeria accessions, whereas most of the west African accessions were associated with most of the Cameroon/Nigeria accessions in the other subpopulation. Comparison with SSR analysis of other Vigna cultigens, i.e., cultivated azuki bean ( Vigna angularis ) and mungbean ( Vigna radiata ), reveals that the mean gene diversity of Bambara groundnut was lower than azuki bean but higher than mungbean.     

Detection of intergenomic translocations with centromeric and noncentromeric breakpoints in Triticum araraticum: mechanism of origin and adaptive significance.

Triticum araraticum Jakubz. (2n = 4x = 28, AtAtGG), a wild progenitor of the polyploid cultivated wheat T. timopheevii, shows extensive chromosome translocation polymorphism in natural populations from the Middle East and Transcaucasia. From an extensive survey, eight intergenomic translocation types were observed and their breakpoints analyzed by genomic in situ hybridization. The previously reported species-specific 6At-1G-4G cyclic translocation was found in all accessions studied. In four translocation types, the breakpoints were in interstitial regions of chromosomes and the other four arose via centric-breakage-fusion. A model is presented on the mechanism of origin and the adaptive significance of translocations with centromeric and noncentromeric breakpoints.     

Genetic structure of a Lima bean base collection using allozyme markers

 Genetic diversity and structure within a Lima bean (Phaseolus lunatus L.) base collection have been evaluated using allozyme markers. The results obtained from the analysis of wild and cultivated accessions confirm the existence of Andean and Mesoamerican gene pools characterised by specific alleles. Wild and cultivated accessions of the same gene pool are grouped. The Andean natural populations have a very limited geographic distribution between Ecuador and northern Peru. The Mesoamerican wild form extends from Mexico up to Argentina through the eastern side of the Andes. Andean and Mesoamerican cultivated accessions of pantropical distribution contribute substantially to the genetic diversity of the Lima bean base collection. Population genetic parameters, estimated from allozymes, confirmed the predominant selfing mating system of the Lima bean. The selfing mating system, the occurrence of small populations, and low gene flow lead to an interpopulation gene diversity (D_ST=0.235) higher than the intrapopulation gene diversity (H_S=0.032). On the basis of the results, guidelines are given to preserve and exploit the genetic diversity of this threatened species. The results also confirm the independent domestication of the Lima bean in at least two centres, one of which is located at medium elevation in the western valleys of Ecuador and northern Peru. Received: 3 June 1997 / Accepted: 17 June 1997     

Identification of genetic variations of cultivated and weedy types of Perilla species in Korea and Japan using morphological and SSR markers

To better understand the genetic diversity and relationships of the two cultivated types of Perilla crop and their weedy types in Korea and Japan, we evaluated the genetic variations of 56 accessions by assessing five morphological characteristics and 18 SSR markers. The two cultivated types of var. frutescens and var. crispa were clearly distinguished by seed size, whereas most accessions of cultivated and weedy types of var. crispa cannot be distinguished strictly by seed characteristics. A total of 165 alleles with the SSR analysis were detected with an average number of 9.2 alleles per locus among the 56 Perilla accessions. The number of alleles per locus ranged from two for KWPE-56 and KWPE-39 to 21 for GBPFM-204. Additionally, the genetic diversity of each locus ranged from 0.497 at KWPE-56 and KWPE-39 to 0.959 at GBPFM-204, with an average of 0.692. The average genetic diversity values were 0.549, 0.685, 0.451 and 0.557 for cultivated and weedy types of var. frutescens and for cultivated and weedy types of var. crispa, respectively. The weedy type accessions of var. frutescens and var. crispa evidenced greater variation than the corresponding cultivated type accessions. The accessions of the cultivated and weedy types of var. frutescens and var. crispa from Korea exhibited greater SSR diversity than those of Japan. An UPGMA phylogenetic tree revealed three major groups, which was congruent with their morphological characteristics except for a few odd accessions. SSR markers clarified the genetic relationships between var. frutescens and var. crispa and helped improve our understanding of the genetic diversity of the two cultivated types of P. frutescens and their weedy types in Korea and Japan.     

Diversity of chloroplast DNA SSRs in wild and cultivated soybeans: evidence for multiple origins of cultivated soybean

Soybean [ Glycine max (L.) Merr.] is one of the major crops in the world and was domesticated from a wild progenitor, Glycine soja Sieb. & Zucc., in East Asia. In order to address the questions concerning the evolution and maternal lineage of soybean, we surveyed the variation in chloroplast DNA simple sequence repeats (cpSSR) of 326 wild and cultivated soybean accessions that were collected from various Asian countries. Twenty-three variants were detected at six cpSSRs in the accessions tested. All of the variants were found in wild soybean, whereas only 14 variants existed in the cultigen. Combining the variants at the six cpSSRs gave 52 haplotypes in the former and eight haplotypes in the latter. Both analyses indicated a considerably higher genetic diversity in the wild soybean. Around 75% of the cultivated accessions tested possessed a common haplotype (no. 49), which was detected in only seven wild accessions, six from southern Japan and one from southern China. The predominant haplotype in the cultigen may therefore have originated from a rare haplotype of the wild soybean that is presently distributed in the southern areas of Japan and China. The remaining seven haplotypes in the cultigen were distributed regionally, and except for three rare haplotypes, largely overlapped with the distributions of wild accessions with the same respective haplotypes. Our results strongly suggest that the cultivated soybeans with different cpDNA haplotypes originated independently in different regions from different wild gene pools and/or hybrid swarms between cultivated and wild forms.     

Mapping of quantitative trait loci for a new source of resistance to bruchids in the wild species Vigna nepalensis Tateishi & Maxted (Vigna subgenus Ceratotropis)

Azuki bean breeders have long been interested in producing azuki bean [Vigna angularis (Willd.) Ohwi & Ohashi] varieties with bruchid resistance. A new bruchid (Callosobruchus spp.) resistance source was found in V. nepalensis Tateishi & Maxted, a species that is cross compatible with azuki bean. Quantitative trait loci (QTLs) analysis for resistance to C. chinensis (L.) and C. maculatus (F.) was conducted using F(2) (V. nepalensis x V. angularis) and BC(1)F(1) [(V. nepalensis x V. angularis) x V. angularis] populations derived from crosses between the bruchid resistant species V. nepalensis and bruchid susceptible species V. angularis. Resistance was measured using two traits, percentage of seeds damaged by bruchids and the time taken for adult bruchids to emerge from seeds. Based on the results from both populations seven QTLs were detected for bruchid resistance; five QTLs for resistance to C. chinensis and two QTLs for resistance to C. maculatus. The different locations found for some resistance QTL to the two bruchid species suggests different resistance mechanisms. QTLs on linkage group (LG) 1 and LG2 for bruchid resistance to C. chinensis co-localized with seed size QTLs suggesting that incremental increase in seed size accompanied susceptibility to C. chinensis. Based on linked markers the QTL on these two linkage groups appear to be the same as previously reported in other Asian Vigna. However, several other QTLs were newly detected including one on LG4 that appears unrelated to seed size. Transfer of these new sources of bruchid resistance from V. nepalensis to azuki bean will be aided by the progress being made in azuki genome mapping.     

Characterization and utilization of microsatellites in the <Emphasis Type="Italic">Coffea canephora</Emphasis> genome to assess genetic association between wild species in Kenya and cultivated coffee

Coffee is an important beverage crop in the world and has a significant contribution to Kenya’s economy. Here, we analyzed the genome-wide distribution of microsatellites in the Coffea canephora genome. A total of 159,041 SSRs were identified, with an overall density of 308 SSRs per Mb. Tetra-nucleotide repeats are the most abundant, accounting for 32 % of the total SSRs. AT-rich motifs are dominant across all SSR repeat units, while GC-rich motifs were generally rare. A set of 100 SSRs was selected to amplify 96 coffee accessions, including 10 wild accessions collected from Mt. Marsabit (Kenya). Of these SSRs, 33 % generated clear polymorphic bands among all tested accessions, with an average of 3.9 alleles per SSR locus. Wild coffee species from Mt. Marsabit showed a close genetic similarity with cultivated accessions in Kenya, suggesting that the wild species in Mt. Marsabit played an important role in the domestication of cultivated coffee in Kenya. Significantly low pairwise genetic divergence was observed between cultivated and wild accessions in Kenya, suggesting a relatively narrow level of genetic basis among coffee germplasm in Kenya. In addition, cultivated and wild coffee accessions in Kenya show a great divergence from those in other countries. Our results not only provide molecular tools for genetic studies in coffee but are also helpful for conservation and coffee breeding programs in Kenya.