Phaseolin-protein Variability in Wild Forms and Landraces of the Common Bean(Phaseolus vulgaris): Evidence for Multiple Centers of Domestication

A sample of 106 wild forms and 99 landraces of common bean (Thaseolus vulgaris) from Middle America and the Andean region of South America were screened for variability in phaseolin seed protein using one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE) and two-dimensional isoelectric focusing SDS/PAGE. The Middle American wild forms exhibited phaseolin patterns similar to the ‘S’ pattern described previously in cultivated forms, as well as a wide variety of additional banding patterns—‘M’ (Middle America) types—not encountered among common bean cultivars. The Andean wild forms showed only the ‘T’ phaseolin pattern, also described previously among cultivated forms. Landraces from Middle America showed ‘S’ or ‘S’-like patterns with the exception of 2 lines with ‘T’ phaseolin. In Andean South America, a majority of landraces had the ‘T’ phaseolin. Additional types represented in that region were (in decreasing order of frequency) the ‘S’ and ‘C’ types (already described among cultivated forms) as well as the ‘H’ (Huevo de huanchaco) and ‘A’ (Ayacucho), (new patterns previously undescribed among wild and cultivated beans). In each region—Middle America and Andean South America—the seeds of landraces with ‘T’ phaseolin were significantly larger than those of landraces with ‘S’ phaseolin. No significant differences in seed size were observed among landraces with ‘T,’ ‘C,’ ‘H,’ and ‘A’ phaseolin types of the Andean region. Our data favor 2 primary areas of domestication, one in Middle America leading to small-seeded cultivars with ‘S’ phaseolin patterns and the other in the Andes giving rise to large-seeded cultivars with ‘T’ (and possibly ‘C,’ ‘H,’ and ‘A’) phaseolin patterns.     

Dissemination pathways of common bean (Phaseolus vulgaris,Fabaceae) deduced from phaseolin electrophoretic variability. I. The Americas

Dissemination pathways of common bean (Phaseolus vulgaris) cultivars from their areas of domestication to other parts of the Americas were determined using phaseolin type, as determined by 1-dimensional SDS/PAGE. Common bean cultivars of lowland South America exhibited approximately equal numbers of ‘S’ and ‘T’ phaseolin types. ‘S2019 cultivars of that region may have been introduced along a route starting in Middle America and leading into Colombia, Venezuela, and eventually Brazil. ‘T’ phaseolin cultivars in lowland South America may have been introduced directly from the Andes or indirectly by European immigrants. In the southwestern U.S.A., most of the cultivars showed an ‘S’ phaseolin, confirming the Middle American origin of these cultivars, as suggested previously by the archaeological record. In northeastern U.S.A. and Canada, the ‘T’and ‘C’ phaseolin types were more frequent than the ‘S’ phaseolin cultivars. While most of the former were possibly introduced into that region by European immigrants, most of the latter may have been introduced by the pre-Columbian Indian populations. Seed size analysis revealed that ‘T’ or ‘C’ phaseolin cultivars had significantly larger seeds than ‘S’ phaseolin cultivars, as had been observed previously in Middle America and the Andes. The phaseolin types of commercial seed types and of early northeastern U.S. cultivars are discussed.     

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.     

Dissemination pathways of common bean (Phaseolus vulgaris,Fabaceae) deduced from phaseolin electrophoretic variability. II. Europe and Africa

Phaseolin type, determined by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis, was used to suggest dissemination routes of common bean (Thaseolus vulgaris) cultivars from their areas of domestication to Europe and Africa. In the Iberian Peninsula, ‘C’ was the most frequent phaseolin type. Only in Chile has a comparably high ‘C’ frequency been observed previously, indicating that many Iberian cultivars may have been introduced from Chile, or that many Chilean cultivars may have come from the Iberian Peninsula. In Europe (outside the Iberian Peninsula), most cultivars exhibited a ‘T’ type. The high frequency of this type may be related to the high frequency of green pod cultivars among European cultivars. Most African cultivars exhibited a ‘T’ or a ‘C’ type and may have been introduced from Brazil, the Iberian Peninsula, or western Europe. ‘T’ or ‘C’ cultivars had larger seeds than ‘S’ cultivars. The phaseolin patterns of cultivars with different seed types and of early French cultivars are discussed.     

中国普通菜豆种质资源朊蛋白变异及多样性分析

朊蛋白是研究普通菜豆遗传多样性的一种重要且有效的生化标记。本试验通过SDS-PAEG凝胶电泳检测中国普通菜豆种质资源的朊蛋白变异类型,分析中国普通菜豆种质资源的遗传多样性及组成特点。来自中国13个省(自治区)的445份供试材料共检测到S、Sb、Sd、B、C、CA、T、PA、To、H、H1、CH 12种朊蛋白类型,表明中国普通菜豆种质朊蛋白变异类型丰富,遗传多样性水平较高。其中,Sb型朊蛋白种质最多,占比29.0%;T型其次,占比28.1%。依据朊蛋白类型在不同基因库的特异性,将研究材料明显地区分为中美基因库和安第斯基因库两大类。研究还发现中国普通菜豆种质资源中地方种质朊蛋白类型变异丰富,多样性明显高于现代育成品种或品系。最后,对种质朊蛋白类型与百粒重、子粒颜色、粒型进行相关性分析,结果表明朊蛋白类型与百粒重呈极显著正相关,而朊蛋白类型与子粒颜色、粒型2个性状之间无明显相关性。本研究结果将为普通菜豆种质资源的保护及有效地挖掘优质种质资源提供理论依据。     

Bean lectins

Summary Seeds of forty bean cultivars having different lectin types based on two-dimensional isoelectric focusing-sodium dodecyl sulfate polyacrylamide gel electrophoresis (IEF-SDS/PAGE) were analyzed for quantities of lectin, phaseolin and total protein. Significant differences were found among groups of cultivars with different lectin types for the quantity of lectin and phaseolin. Cultivars with more complex lectin types based on IEF-SDS/PAGE tended to have higher quantities of lectin and lower quantities of phaseolin than cultivars with simple lectin types. An association between lectin type and the quantity of lectin and phaseolin was found also in the seeds of F₂ plants that segregated in a Mendelian fashion for two lectin types. Seeds from plants with the complex lectin type had more lectin and less phaseolin than seeds from plants with the simple lectin type. Therefore, the genes controlling qualitative lectin variation also may influence the quantitative variation of lectin and phaseolin. The results of this study are related to other studies on the quantitative variation for seed proteins and to the possible molecular basis for variation in the quantity of lectins in beans.     

Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity

Summary Allozyme analysis was performed on 83 wild Phaseolus vulgaris accessions, representing a wide geographical distribution from Mesoamerica to Argentina, to determine levels of genetic diversity and geographic patterns of variability at nine polymorphic isozyme loci. The collection can be divided into two major groups, one consisting of accessions from Mexico, Central America, Colombia and Peru, and the other consisting of accessions from Peru and Argentina. One accession from northern Peru is distinct from the two major groups, and may delineate a transition zone between the two divergent groups. The level of genetic diversity within wild P. vulgaris (Ht=0.132) is comparable with those found in other Phaseolus species. There was no significant within-accession gene diversity (Hs=0.006); however, there is a moderate level of genetic diversity (Dst=0.126) between accessions. Our results are consistent with previous studies on the genetic diversity of wild P. vulgaris using phaseolin, the major seed storage protein of beans.     

Bean arcelin

Summary Crude proteins from seeds of wild bean accessions of Mexican origin were analyzed by one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS/PAGE). Several accessions had electrophoretic patterns showing unique protein bands. When analyzed by two-dimensional isoelectric focusing (IEF)-SDS/PAGE, four protein variants which had electrophoretic mobilities similar to each other but different from the other major seed proteins, phaseolin and lectin, were observed. All four variants, which have not been described in cultivated beans, were tentatively named arcelin proteins and designated as arcelin 1, 2, 3 and 4. Arcelins 3 and 4 had polypeptides that comigrated on two-dimensional gels and these variants occurred in accessions that were collected in the same location. Analysis of single F₂ seeds from crosses among arcelin-containing lines and from crosses between cultivated beans lines without arcelin and arcelin-containing lines revealed that differences in arcelin polypeptide expression were inherited monogenically. The alleles for different arcelin variants were codominant to each other and dominant to the absence of arcelin. The gene(s) controlling arcelin proteins were unlinked to those controlling phaseolin expression and tightly linked to genes controlling the presence of lectin proteins (< 0.30% recombination). The possible origins of arcelin genes and their potential role in bruchid resistance are discussed.     

Ecogeographic distribution ofPhaseolus spp. (Fabaceae) in Bolivia

WildPhaseolus vulgaris is distributed between northern Mexico and northern Argentina. Analysis of phaseolin and molecular markers (isozymes, Restriction Fragment Length Polymorphisms or RFLPs) indicate that this gene pool consists of two major groups, Mesoamerican and Andean, and a third intermediate group found in northwestern South America. Previous to this study, only four accessions of wildP. vulgaris beans from Bolivia had been collected and their genetic relationship with other wild beans from Latin America was not known. Due to the problem of intense erosion in some areas of Bolivia, it was our objective to survey and documentPhaseolus spp. in this area before their extinction. We conducted a collection expedition in May 1994 in the departments of Cochabamba, Chuquisaca and Tarija. This resulted in collections of four populations ofP. augusti, two of cultivatedP. lunatus and two mixtures of cultivatedP. vulgaris. The first mixture was made of “k’opurus” or beans consumed after toasting, and represented an addition of 17 accessions to the Bolivian collection. The second mixture was made of “porotos” and resulted in the addition of 10 new accessions. Seven germplasm collections of wildP. vulgaris were found, which allowed us to increase the number of known populations of wild common bean for Bolivia. Another accession was found as a wild-weed-crop complex. Seven of these wildP. vulgaris accessions along with another accession from Bolivia collected previously, and a number of P. vulgaris accessions from Mexico (17), Guatemala (3), Colombia (10), Ecuador (6), Peru (17) and Argentina (16) were analyzed with RAPDs. The use of 14 random primers and one SCAR (Sequence Characterized Amplified Region) resulted in 90 bands, of which 83 were polymorphic. This data was used to construct a dendrogram which shows clear separation into three clusters, corresponding to each of the gene pools and an intermediate group. The Bolivian wild P. vulgaris beans grouped with the accessions of southern Peru and Argentina into the Andean gene pool. RAPD analysis of genetic diversity correlated well with genetic diversity obtained with other markers. Moreover, the ease of analysis allowed us to obtain a large number of bands which was conducive to greater sensitivity and identification of geographic subgroups and accessions of hybrid origin.     

Observations on the origin of phaseolus polyanthus Greenman

Total seed protein variability in a sample of 163 entries of year-bean (Phaseolus polyanthus), including wild, feral and cultivated forms of the whole range of distribution in Latin America was studied using I-dimensional SDS/PAGE and 2-dimensional IEF-SDS/PAGE. Ten different patterns were observed in this crop. Eight of these are found in the Mesoamerican materials, the other two of those in the northern Andes. The highest diversity is found in the wild ancestral forms present in central Guatemala with six patterns. The ‘b’pattern predominant in all Mesoamerican cultivated materials is also present at low frequency in Colombia. The ‘k’ pattern, predominant in the northern Andes, is present in Costa Rica. These results together with information on indigenous names for the crop suggest that there is a single gene pool domesticated from a wild ancestor still present in Guatemala, and distributed afterwards to the northern Andes, but with a clinal genetic drift from Mesoamerica to the Andean region.     

DNA restriction fragment length polymorphisms correlate with isozyme diversity in Phaseolus vulgaris L.

Summary Genetic variation in Phaseolus vulgaris L. (P. vulgaris) was investigated at the isozyme and DNA levels. We constructed a library of size-selected Pst I clones of P. vulgaris nuclear DNA. Clones from this library were used to examine 14 P. vulgaris accessions for restriction fragment length polymorphisms (RFLPs). DNAs from each accession were analyzed with three restriction enzymes and 18 single copy probes. The same accessions were also examined for variability at 16 isozyme loci. Accessions included four representatives of the T phaseolin group and five representatives each of the C and S phaseolin groups. One member of the S group (the breeding line XR-235-1-1) was derived from a cross between P. vulgaris and P. coccineus. Isozymes and RFLPs revealed very similar patterns of genetic variation. Little variation was observed among accessions with C and T phaseolin types or among those with the S phaseolin type. However, both isozyme and RFLP data grouped accessions with S phaseolin separately from those accessions with C or T phaseolin. The highest degree of polymorphism was observed between XR-235-1-1 and members of the C/T group. RFLP markers will supplement isozymes, increasing the number of polymorphic loci that can be analyzed in breeding, genetic, and evolutionary studies of Phaseolus.     

Phaseolin seed variability in common bean (Phaseolus vulgaris L.) by capillary gel electrophoresis

Phaseolin, the major seed storage protein of Phaseolus vulgaris from forty-four wild and cultivated accessions, was studied using sodium dodecyl sulphate-capillary gel electrophoresis (SDS-CGE). In total, eleven phaseolin profiles, revealing polypeptide subunit variation in the range from 45.6 kDa to 54.4 kDa, were recorded. The number of polypeptide subunits recorded in particular profiles varied from 3 to 6; in total, eight phaseolin subunits were distinguished in the examined material. Ferguson plot analysis was used to correct non-ideal behaviour of phaseolin polypeptide subunits in capillary gel electrophoresis in the presence of SDS. The obtained results are compared to electrophoretic data received by slab polyacrylamide gel electrophoresis. The SDS-CGE method appears to provide a powerful tool for disclosure of phaseolin subunit variability.     

Effects of low temperature on wheat leaf proteins

Finnish wheat cultivars, winter wheat ‘Vakka’ and spring wheat ‘Apu’, grown for 9 days at 25° and then for 52 days at 2–4°, were called ‘hardened’. Proteins and esterases of young leaves were resolved by polyacrylamide gel electrophoresis (PAGE), porosity gradient PAGE (poroPAGE), isoelectric focusing (PAGIF) between pH 3 and 9, and by Na-dodecylsulfate (SDS)-PAGE. Hardened and unhardened leaves have different protein patterns after PAGE, PAGIF, poroPAGE and SDS-PAGE, respectively, as well as for esterases after PAGE and PAGIF. The PAGIF patterns of esterases show distinct changes of two bands especially for hardened leaves of winter wheat, one appearing, the other one disappearing.     

Development of a CAPS marker system for genotyping European pear cultivars harboring 17 <Emphasis Type="Italic">S</Emphasis> alleles

The full-length cDNAs of eight S ribonucleases (S-RNases) were cloned from stylar RNA of European pear cultivars that could not be characterized by the cleaved amplified polymorphic sequences (CAPS) marker system for genotyping European pear cultivars harboring nine S alleles Sa, Sb, Sd, Se, Sh, Sk, Sl, Sq, and Sr. Comparison of the nucleotide sequences between these cDNAs and six putative S-RNase alleles previously amplified by genomic PCR revealed that five corresponded to the putative Sc-, Si-, Sm-, Sn-, and Sp-RNase alleles and the other three corresponded new S-RNase alleles (designated as putative Sg-, Ss-, and St-RNase alleles). Genomic PCR with a new set of primers was used to amplify 17 S-RNase alleles: 1906 bp (Sg), 1642 bp (St), 1414 bp (Sl), ca. 1.3 kb (Sk and Sq), 998 bp (Se), 440 bp (Sb), and ca. 350 bp (Sa, Sc, Sd, Sh, Si, Sm, Sn, Sp, Sr, and Ss). Among them, S-RNase alleles of similar size were discriminated by digestion with 11 restriction endo-nucleases. The PCR amplification of 17 S-RNase alleles following digestion with the restriction endonucleases provided a new CAPS marker system for rapid S-genotyping of European pear cultivars harboring 17 S alleles. Using the CAPS analysis, Sc, Sg, Si, Sm, Sn, Sp, Ss, and St alleles were found in 32 cultivars, which were classified into 23 S-genotypes.     

Evidence for Introduction Bottleneck and Extensive Inter-Gene Pool (Mesoamerica x Andes) Hybridization in the European Common Bean (Phaseolus vulgaris L.) Germplasm

Common bean diversity within and between Mesoamerican and Andean gene pools was compared in 89 landraces from America and 256 landraces from Europe, to elucidate the effects of bottleneck of introduction and selection for adaptation during the expansion of common bean (Phaseolus vulgaris L.) in Europe. Thirteen highly polymorphic nuclear microsatellite markers (nuSSRs) were used to complement chloroplast microsatellite (cpSSRs) and nuclear markers (phaseolin and Pv-shatterproof1) data from previous studies. To verify the extent of the introduction bottleneck, inter-gene pool hybrids were distinguished from “pure” accessions. Hybrids were identified on the basis of recombination of gene pool specific cpSSR, phaseolin and Pv-shatterproof1 markers with a Bayesian assignments based on nuSSRs, and with STRUCTURE admixture analysis. More hybrids were detected than previously, and their frequency was almost four times larger in Europe (40.2%) than in America (12.3%). The genetic bottleneck following the introduction into Europe was not evidenced in the analysis including all the accessions, but it was significant when estimated only with “pure” accessions, and five times larger for Mesoamerican than for Andean germplasm. The extensive inter-gene pool hybridization generated a large amount of genotypic diversity that mitigated the effects of the bottleneck that occurred when common bean was introduced in Europe. The implication for evolution and the advantages for common bean breeding are discussed.     

Evolution of genetic diversity during the domestication of common-bean (Phaseolus vulgaris L.)

M13 DNA fingerprinting was used to determine evolutionary changes that occurred in Latin American germ plasm and USA cultivars of commonbean (Phaseolus vulgaris L.) during domestication. Linkage mapping experiments showed that M13-related sequences in the common-bean genome were either located at the distal ends of linkage groups or that they were unlinked to each other or to any previously mapped markers. Levels of polymorphism observed by hybridization with M13 (1 probe-enzyme combination) were comparable to those observed by hybridization with single-copy random PstI genomic probes (36 enzyme-probe combinations) but were higher than those observed for isozymes (10 loci). Results indicated that the wild ancestor had diverged into two taxa, one distributed in Middle America (Mexico, Central America, and Colombia) and the other in the Andes (Peru and Argentina); they also suggested separate domestications in the two areas leading to two cultivated gene pools. Domestication in both areas led to pronounced reductions in diversity in cultivated descendants in Middle America and the Andes. The marked lack of polymorphism within commercial classes of USA cultivars suggests that the dispersal of cultivars from the centers of origin and subsequent breeding of improved cultivars led to high levels of genetic uniformity. To our knowledge, this is the first crop for which this reduction in diversity has been documented with a single type of marker in lineages that span the evolution between wild ancestor and advanced cultivars.     

Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.).

Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A-H) based on insertion-deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogon - O. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogon - O. nivara complex.     

Evidence for phosphorylation of the major seed storage protein of the common bean and its phosphorylation-dependent degradation during germination

Phaseolin is the major seed storage protein of common bean, Phaseolus vulgaris L., accounting for up to 50 % of the total seed proteome. The regulatory mechanisms responsible for the synthesis, accumulation and degradation of phaseolin in the common bean seed are not yet sufficiently known. Here, we report on a systematic study in dormant and 4-day germinating bean seeds from cultivars Sanilac (S) and Tendergreen (T) to explore the presence and dynamics of phosphorylated phaseolin isoforms. High-resolution two-dimensional electrophoresis in combination with the phosphoprotein-specific Pro-Q Diamond phosphoprotein fluorescent stain and chemical dephosphorylation by hydrogen fluoride–pyridine enabled us to identify differentially phosphorylated phaseolin polypeptides in dormant and germinating seeds from cultivars S and T. Phosphorylated forms of the two subunits of type α and β that compose the phaseolin were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) and MALDI-TOF/TOF tandem MS. In addition, we found that the levels of phosphorylation of the phaseolin changed remarkably in the seed transition from dormancy to early germination stage. Temporal changes in the extent of phosphorylation in response to physiological and metabolic variations suggest that phosphorylated phaseolin isoforms have functional significance. In particular, this prospective study supports the hypothesis that mobilization of the phaseolin in germinating seeds occurs through the degradation of highly phosphorylated isoforms. Taken together, our results indicate that post-translational phaseolin modifications through phosphorylations need to be taken into consideration for a better understanding of the molecular mechanisms underlying its regulation.     

Molecular circumscription of the blackfly Simulium oyapockense from South America

Problems related to the identity of Simuliidae species are impediments to effective disease control in Amazonia. Some of these species, such as Simulium oyapockense Floch & Abonnenc, 1946 (Diptera: Simuliidae), are vectors of the organisms that cause onchocerciasis and mansonellosis diseases. This blackfly species has a wide distribution in South America, and it is suspected of being a complex of cryptic species. The aim of this study is to characterize the nominal species S. oyapockense using partial COI gene sequences. Seven populations of S. oyapockense (morphologically identified) were analysed, including one from its type-locality. The other six populations were collected in Brazil and in Argentina. A taxon collected in Amazonas state, Brazil, with adults similar to S. oyapockense but with distinct pupae, was also included in the analysis (Simulium ‘S’). The nominal species S. oyapockense is circumscribed, and its geographical distribution is restricted to areas north of the Amazon River. Populations of S. oyapockense s.l. collected south of the Amazon River comprise a species complex that needs to be evaluated using integrative taxonomy. Simulium ‘S’ represents a species with unique morphological and molecular characteristics. Distinguishing cryptic species is a prerequisite for reducing the taxonomic impediment, especially in medically important taxa.     

Study on chloroplast DNA diversity of cultivated and wild pears (<Emphasis Type="Italic">Pyrus</Emphasis> L.) in Northern China

Eight pairs of chloroplast DNA (cpDNA) universal primers selected from 34 pairs were used to assess the genetic diversity of 132 pear accessions in Northern China. Among them, six amplified cpDNA fragments showed genetic diversity. A total of 24 variable sites, including 1 singleton variable site and 23 parsimony informative sites, as well as 21 insertion-deletion fragments, were obtained from the combined cpDNA sequences (5309–5535 bp). Two trnL-trnF-487 haplotypes, five trnL-trnF-413 haplotypes, five rbcL haplotypes, six trnS-psbC haplotypes, eight accD-psaI haplotypes and 12 rps16-trnQ haplotypes were identified among the individuals. Twenty-one haplotypes were identified based on the combined fragments. The values of nucleotide diversity (P_i), average number of nucleotide differences (k) and haplotype diversity (H_d) were 0.00070, 3.56408 and 0.7960, respectively. No statistical significance was detected in Tajima’s D test. Remarkably, the important cpDNA haplotypes and their representing accessions were identified clearly in this study. H_19 was considered as one of the ancient haplotypes and was a divergent centre. H_16 was the most common haplotype of the wild accessions. H_2 was the haplotype representing the most pear germplasm resources (46 cultivars and two wild Ussurian Pear accessions), followed by haplotype H_5 (30 cultivars, two wild Ussurian Pear accessions and four sand pears in outgroups) representing the cultivars ‘Dangshan Suli’ and ‘Yali’, which harbour the largest and the second largest cultivation areas in China. More importantly, this study demonstrated, for the first time, the supposed evolution routes of Pyrus based on cpDNA divergence in the background of pear phylogeny in Northern China.