Geographical Ecocline Polymorphism of the Distribution of Mitochondrial Haplotypes of <Emphasis Type="Italic">Adalia bipunctata</Emphasis> Linnaeus, 1758 (Coleoptera: Coccinellidae) of Norway

Adalia bipunctata Linnaeus, 1758 is a classical object for studying polymorphism of natural populations. Application of genetic markers significantly increased the possibilities of analysis of natural populations of ladybirds and opened the possibility of studying ecological adaptations at the genetic level. We analyze the geographical distribution of the mitochondrial haplotypes of A. bipunctata, determined on the basis of the variability of the mitochondrial cox1 gene in the natural populations of Norway. Two new mitochondrial haplotypes of A. bipunctata are described. We observe a geographical cline in the haplotypes frequencies from south to north. The main haplotype H1 of the central Europe is gradually replaced in the north by the haplotype H7. A possible reason for the observed geographical cline is a selective advantage of beetles with haplotype H7 in areas with a northern coastal climate.     

A spatially explicit analysis of <Emphasis Type="Italic">Paysandisia archon</Emphasis> attack on the endemic Mediterranean dwarf palm

Autochthonous plant species are heavily threatened by the increasing spread of invasive insects. The spatial distribution of invasive species’ hosts is likely to play a pivotal role in the establishment and further expansion of the invading species; more specifically, distance and density dependent (DDD) processes linked to plant spatial arrangement are crucial in determining susceptibility to attack, but they have usually been overlooked in invasive research. We take a spatially explicit approach to evaluate potential DDD processes in the interaction between Paysandisia archon, a tropical lepidopteran recently introduced in Spain, and the endemic Mediterranean dwarf palm (Chamaerops humilis) in Mallorca (Balearic Islands). Specifically, we used spatial marked point pattern analyses, which allowed testing whether DDD processes affect attack probability and intensity on three dwarf palm populations corresponding to three different invasion phases (i.e., infestation core, early expansion, and expansion front). Our approach also allowed evaluation of whether and how intrinsic palm traits (size, sex) alter the proneness to P. archon attack over a range of spatial scales. The occurrence and nature of DDD effects on C. humilis performance varied largely among localities. At the infestation core, our analyses revealed positive density dependence, i.e., reduced damage at high densities or proximity to conspecific neighbors. By contrast, the early expansion locality showed negative density dependence of C. humilis performance, whereas at the expansion front, there was no evidence of DDD effects. Larger palms were consistently more prone to P. archon attack than small ones up to scales of 50 m. We found no evidence that palm sex altered the probability of attack by P. archon. Our results highlight the importance of spatially explicit analyses for assessing invasive events and point to the need of early interventions and prioritizing management efforts on larger palms in order to guarantee the conservation of autochthonous dwarf palm populations.     

Cystic fibrosis in Afro-Brazilians: <Emphasis Type="Italic">XK</Emphasis> haplotypes analysis supports the European origin of <Emphasis Type="Italic">p.F508del</Emphasis> mutation

Cystic fibrosis (CF) is a common autosomal recessive disorder, being the p.F508del the most frequent mutation. Also, a nearby restriction fragment length polymorphism (RFLP) named XK (KM19 and XV2C) is non-randomly associated with specific CF alleles. Our aim was to analyze the occurrence of the p.F508del mutation and XK haplotypes in Afro-Brazilians CF patients and controls, since these data is available for the other two main ethnic groups found in Brazil (Euro-Brazilians and Brazilian Amerindians), contributing for the whole comprehension of these haplotypes in the Brazilian population. A total of 103 patients and 54 controls were studied. PCR and PCR-RFLP methodologies were used to identify the presence of the p.F508del and the XK haplotype in the subjects. The combined data show that 84.2% of p.F508del mutation is associated with haplotype B and only 15.8% with haplotype A; no other haplotypes were found to be associated with this mutation. Our data suggest that the occurrence of p.F508del mutation and haplotype B in Afro-Brazilian patients occurs probably due to admixture with Euro-descendants. Therefore this mutation and haplotype could be used as a admixture marker.     

Nucleotide sequence analysis of <Emphasis Type="Italic">S</Emphasis>-locus genes to unify <Emphasis Type="Italic">S</Emphasis> haplotype nomenclature in radish

Radish, belonging to the family Brassicaceae, has a self-incompatibility which is controlled by multiple alleles on the S locus. To employ the self-incompatibility in an F₁ breeding system, identification of S haplotypes is necessary. Since collection of S haplotypes and determination of nucleotide sequences of SLG, SRK, and SCR alleles in cultivated radish have been conducted by different groups independently, the same or similar sequences with different S haplotype names and different sequences with the same S haplotype names have been registered in public databases, resulting in confusion of S haplotype names for researchers and breeders. In the present study, we developed S homozygous lines from radish F₁ hybrid cultivars in Japan and determined the nucleotide sequences of SCR, the S domain and the kinase domain of SRK, and the SLG of a large number of S haplotypes. Comparing these sequences with our previously published sequences, the haplotypes were ordered into 23 different S haplotypes. The sequences of the 23 S haplotypes were compared with S haplotype sequences registered by different groups, and we suggested a unification of these S haplotypes. Furthermore, dot-blot hybridization using SRK allele-specific probes was examined for developing a standard method for S haplotype identification.     

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.     

Molecular data reveal the hybrid nature of an introduced population of banded newts (<Emphasis Type="Italic">Ommatotriton</Emphasis>) in Spain

The three species of banded newt (genus Ommatotriton) are endemic to the Near East. Recently an introduced banded newt population was discovered in Catalonia, Spain. To determine the species involved and the geographical source, we genotyped 11 individuals for one mitochondrial and two nuclear genetic markers, and compared the observed haplotypes to a range-wide phylogeography of Ommatotriton. All haplotypes identified in Spain are identical to haplotypes known from the native range. The mitochondrial haplotypes derive from O. ophryticus and were originally recorded in northeast Turkey. The nuclear haplotypes reveal that all individuals are genetically admixed between O. ophryticus and O. nesterovi. While the geographical resolution for the nuclear markers is low, the source of the O. nesterovi ancestry must be Turkey, as this species is a Turkish endemic. Species distribution models suggest a large potential distribution for the two Ommatotriton species, extending over northern Iberia and southern France. The ecology of hybrids can differ substantially from that of the parent species, making the impact of the Spanish hybrid banded newt population difficult to predict.     

Identification and genetic diversity of two invasive <Emphasis Type="Italic">Pissodes</Emphasis> spp. Germar (Coleoptera: Curculionidae) in their introduced range in the southern hemisphere

During the first half of the twentieth century, two accidental cases of introduction of Pissodes weevils were recorded from the southern hemisphere. The weevils in South Africa were identified as the deodar weevil (Pissodes nemorensis) and those in South America as the small banded pine weevil (Pissodes castaneus). Wide distribution of the two species in their invasive range, general difficulty in identifying some Pissodes spp., and the varying feeding and breeding behaviours of the species in South Africa has necessitated better evidence of species identity and genetic diversity of both species and population structure of the species in South Africa. Barcoding and the Jerry-to-Pat region of the COI gene were investigated. Morphometric data of the South African species was analysed. Our results confirmed the introduction of only one Pissodes species of North American origin to South Africa. However, this species is not P. nemorensis, but an unrecognized species of the P. strobi complex or a hybrid between P. strobi and P. nemorensis. Only P. castaneus, of European origin, was identified from South America. We identified ten mitochondrial DNA haplotypes from South Africa with evidence of moderate genetic structure among geographic populations. Terminal leader and bole-feeding weevils did not differ at the COI locus. A single haplotype was identified from populations of P. castaneus in South America. Results of the present study will have implications on quarantine, research and management of these insect species.     

<Emphasis Type="Italic">Bruguiera hainesii</Emphasis>, a critically endangered mangrove species,is a hybrid between <Emphasis Type="Italic">B. cylindrica</Emphasis> and <Emphasis Type="Italic">B. gymnorhiza</Emphasis> (Rhizophoraceae)

Bruguiera hainesii (Rhizophoraceae) is one of the two Critically Endangered mangrove species listed in the IUCN Red List of Threatened Species. Although the species is vulnerable to extinction, its genetic diversity and the evolutionary relationships with other Bruguiera species are not well understood. Also, intermediate morphological characters imply that the species might be of hybrid origin. To clarify the genetic relationship between B. hainesii and other Bruguiera species, we conducted molecular analyses including all six Bruguiera species using DNA sequences of two nuclear genes (CesA and UNK) and three chloroplast regions (intergenic spacer regions of trnL-trnF, trnS-trnG and atpB-rbcL). For nuclear DNA markers, all nine B. hainesii samples from five populations were heterozygous at both loci, with one allele was shared with B. cylindrica, and the other with B. gymnorhiza. For chloroplast DNA markers, the two haplotypes found in B. hainesii were shared only by B. cylindrica. These results suggested that B. hainesii is a hybrid between B. cylindrica as the maternal parent and B. gymnorhiza as the paternal one. Furthermore, chloroplast DNA haplotypes found in B. hainesii suggest that hybridization has occurred independently in regions where the distribution ranges of the parental species meet. As the IUCN Red List of Threatened Species currently excludes hybrids (except for apomictic plant hybrids), the conservation status of B. hainesii should be reconsidered.     

Identification of birch pollen species using FTIR spectroscopy

In this study, the morphology and chemical composition of pollen grains of six birch species (Betula utilis Doorenbos, B. dahurica, B. maximowicziana, B. pendula, B. pubescens and B. humilis) were examined to verify which of these features allow distinguishing them in a more unambiguous way. For this purpose, scanning electron microscopy and light microscopy, as well as Fourier transform infrared (FTIR) spectroscopy and curve-fitting analysis of amide I profile, were performed. The microscopy images show that the pollen grains of B. pubescens, B. pendula and B. humilis are similar in diameter and significantly smaller than those of others species, with the largest diameter observed for B. utilis Doorenbos. However, the results obtained from FTIR spectroscopy indicate that the chemical compositions of B. pubescens and B. pendula are similar, but B. humilis is outlaying. Summarizing, it is not possible to unambiguously state, which feature or which technique is the best for differentiating between the six chosen birch species. However, the study showed that both techniques have potential for identification of birch pollen species.     

<Emphasis Type="Italic">Spartina versicolor</Emphasis> Fabre: Another case of <Emphasis Type="Italic">Spartina</Emphasis> trans-Atlantic introduction?

Intercontinental introductions are widespread in the genus Spartina, with important ecological and evolutionary consequences. The native or introduced status of Spartina species is then critical with regard to biodiversity assessment, especially for vulnerable Mediterranean coastline ecosystems. Spartina versicolor was first recorded in southern France in 1849, then successively in various places on the European and North-African Mediterranean and Atlantic coasts. This species is considered to be either a European native or an invasive species introduced from North America which has a high morphological similarity to the Atlantic American species Spartina patens. We performed extensive sampling of S. versicolor in Europe and North Africa (from natural populations and herbarium collections) and compared these samples to other European and American Spartina species (including S. patens). Chromosome counts were reported for the first time and revealed that S. versicolor is tetraploid (2n = 4x = 40). Phylogenetic analyses based on chloroplast and nuclear ribosomal DNA sequences did not reveal any molecular variation within S. versicolor. In this species, a single haplotype, that is identical to one haplotype of S. patens, was found in the four chloroplast and the nuclear ribosomal ITS regions investigated. In addition, simple sequence repeat markers were used and revealed a low level of genetic diversity within S. versicolor, suggesting that the introduction of S. versicolor occurred from a narrow genetic pool of S. patens from North America.     

Hytrosavirus genetic diversity and eco-regional spread in <Emphasis Type="Italic">Glossina</Emphasis> species

Background

The management of the tsetse species Glossina pallidipes (Diptera; Glossinidae) in Africa by the sterile insect technique (SIT) has been hindered by infections of G. pallidipes production colonies with Glossina pallidipes salivary gland hypertrophy virus (GpSGHV; Hytrosaviridae family). This virus can significantly decrease productivity of the G. pallidipes colonies. Here, we used three highly diverged genes and two variable number tandem repeat regions (VNTRs) of the GpSGHV genome to identify the viral haplotypes in seven Glossina species obtained from 29 African locations and determine their phylogenetic relatedness.

Results

GpSGHV was detected in all analysed Glossina species using PCR. The highest GpSGHV prevalence was found in G. pallidipes colonized at FAO/IAEA Insect Pest Control Laboratory (IPCL) that originated from Uganda (100%) and Tanzania (88%), and a lower prevalence in G. morsitans morsitans from Tanzania (58%) and Zimbabwe (20%). Whereas GpSGHV was detected in 25–40% of G. fuscipes fuscipes in eastern Uganda, the virus was not detected in specimens of neighboring western Kenya. Most of the identified 15 haplotypes were restricted to specific Glossina species in distinct locations. Seven haplotypes were found exclusively in G. pallidipes. The reference haplotype H1 (GpSGHV-Uga; Ugandan strain) was the most widely distributed, but was not found in G. swynnertoni GpSGHV. The 15 haplotypes clustered into three distinct phylogenetic clades, the largest contained seven haplotypes, which were detected in six Glossina species. The G. pallidipes-infecting haplotypes H10, H11 and H12 (from Kenya) clustered with H7 (from Ethiopia), which presumably corresponds to the recently sequenced GpSGHV-Eth (Ethiopian) strain. These four haplotypes diverged the most from the reference H1 (GpSGHV-Uga). Haplotypes H1, H5 and H14 formed three main genealogy hubs, potentially representing the ancestors of the 15 haplotypes.

Conclusion

These data identify G. pallidipes as a significant driver for the generation and diversity of GpSGHV variants. This information may provide control guidance when new tsetse colonies are established and hence, for improved management of the virus in tsetse rearing facilities that maintain multiple Glossina species.

     

Phylogenetic relationships among cultivated <Emphasis Type="Italic">Zanthoxylum</Emphasis> species in China based on cpDNA markers

We here present a molecular phylogenetic analysis of cultivated Zanthoxylum species which have a long history of cultivation both for economic and for chemical values in China. Three cpDNA markers, including matK, rbcL, and trnL-F, were sequenced, with the goals of untangling phylogenetic relationships and inferring biogeographic origin and patterns of distribution among Zanthoxylum species. Based on three cpDNA markers, 19 haplotypes with 64 polymorphic sites in Zanthoxylum provenances were identified in our study. A low genetic differentiation (G _ST ?=?0.271, N _ST ?=?0.373) was observed within Zanthoxylum provenances. Based on phylogenetic tree and haplotype network, all 19 haplotypes were grouped into six clusters. Our results also supported the hypothesis that the so-called “Green Huajiao” belongs to the species Zanthoxylum armatum rather than Zanthoxylum schinifolium. The results also revealed that haplotypes of two cultivated species, Zanthoxylum bungeanum and Z. armatum, most probably diverged during the Late Miocene. Ancestral area reconstruction indicated that cultivated Zanthoxylum species experienced multiple long-distance dispersal events and several vicariance events and the ancestors of Zanthoxylum first colonized Yunnan and Guizhou provinces (D). Accordingly, the current disjunct distribution of Z. bungeanum and Z. armatum may represent long-distance dispersal of ancestors popularly named “Dahongpao” and “Qinghuajiao,” respectively. It is concluded that cpDNA markers may provide a new conceptual and practical opportunity to evaluate genetic diversity and to identify local cultivars of Zanthoxylum, making it a valuable source to include into potential breeding programs.     

The invasion biology of the invasive earwig, <Emphasis Type="Italic">Forficula auricularia</Emphasis> in Australasian ecosystems

The European earwig, Forficula auricularia, is a cosmopolitan insect endemic to Europe, West Asia and North Africa, which has invaded many temperate regions of the world including Australia and New Zealand. F. auricularia has been shown to be a complex of morphologically identical, reproductively isolated lineages that possess two distinct clades of mitochondrial DNA. Entomological collection data, historical literature and further field collections were used to develop a greater understanding of Australian F. auricularia’s invasion biology and its current distribution. Genetic analysis of F. auricularia collected from Australia and New Zealand using two mitochondrial genes (COI and a fragment overlapping parts of the COI -COII genes) was also undertaken. To identify the possible source populations of the Australasian invasion these sequences were compared to those from 16 locations within Britain and continental Europe. All Australasian populations were shown to be of the clade B lineage. Tasmanian and New Zealand populations consist of a single subclade comprised of only 4 and 1 haplotypes respectively. The Australian mainland populations also contained a second subclade consisting of up to 11 haplotypes indicating that multiple introductions possibly occurred on the Australian mainland. Comparison of mitochondrial genomes from Australasian and European populations showed the Australian mainland subclade to be most closely related to Portuguese haplotypes, and the Tasmanian and New Zealand clade closely related to those in Brittany, France. No European haplotypes perfectly matched the Australasian sequences. Therefore, the original source populations are still to be identified with harbours on the Iberian Peninsula’s western coast and those on the English Channel likely candidate areas.     

Phylogeography of the Ibero-Maghrebian red-eyed grass snake (<Emphasis Type="Italic">Natrix astreptophora</Emphasis>)

We examined phylogeographic differentiation of the red-eyed grass snake (Natrix astreptophora) using 1984 bp of mtDNA and 13 microsatellite loci from specimens collected across its distribution range in southwestern Europe and northwestern Africa. Based on phylogenetic analyses of mtDNA, European N. astreptophora constituted the sister clade to a weakly supported North African clade comprised of two deeply divergent and well-supported clades, one corresponding to Moroccan snakes and the other to snakes from Algeria and Tunisia. This tripartite differentiation was confirmed by analyses of microsatellite loci. According to a fossil-calibrated molecular clock, European and North African N. astreptophora diverged 5.44 million years ago (mya), and the two Maghrebian clades split 4.64 mya. These dates suggest that the radiation of the three clades was initiated by the environmental changes related to the Messinian Salinity Crisis and the reflooding of the Mediterranean Basin. The differentiation of N. astreptophora, with distinct clades in the Iberian Peninsula and in the western and eastern Maghreb, corresponds to a general phylogeographic paradigm and resembles the differentiation found in another co-distributed Natrix species, the viperine snake (N. maura). Despite both species being good swimmers, the Strait of Gibraltar constitutes a significant biogeographic barrier for them. The discovery that North Africa harbours two endemic lineages of N. astreptophora necessitates more conservation efforts for these imperilled snakes.     

What can the geographic distribution of mtDNA haplotypes tell us about the invasion of New Zealand by house mice <Emphasis Type="Italic">Mus musculus</Emphasis>?

We mapped the distribution and diversity of mitochondrial D-loop haplotypes among 502 New Zealand house mice (Mus musculus). By widespread sampling from 74 sites, we identified 14 new haplotypes. We used Bayesian phylogenetic reconstructions to estimate the genetic relationships between the New Zealand representatives of Mus musculus domesticus (all six known clades) and M. m. castaneus (clade HG2), and mice from other locales. We defined four distinct geographic regions of New Zealand with differing haplotype diversity indices. Our Results suggest (a) two independent pre-1840 invasions by mice of different origin (domesticus clade E and castaneus clade HG2) at opposite ends of the country; (b) multiple later invasions by domesticus clades E and F accompanying the post-1840 development of New Zealand port facilities in the central regions, plus limited local incursions by domesticus clades A, B, C and D1; (c) a separate invasion of Chatham I. by castaneus clade HG2; (d) previously undescribed New Zealand haplotypes, potentially the products of localised indigenous mutation, and (e) hybridisation between different lineages.     

Phylogeographical structure inferred from cpDNA sequence variation of <Emphasis Type="Italic">Zygophyllum xanthoxylon</Emphasis> across north-west China

Zygophyllum xanthoxylon, a desert species, displaying a broad east–west continuous distribution pattern in arid Northwestern China, can be considered as a model species to investigate the biogeographical history of this region. We sequenced two chloroplast DNA spacers (psbK-psbI and rpl32-trnL) in 226 individuals from 31 populations to explore the phylogeographical structure. Median-joining network was constructed and analysis of AMOVA, SMOVA, neutrality tests and distribution analysis were used to examine genetic structure and potential range expansion. Using species distribution modeling, the geographical distribution of Z. xanthoxylon was modeled during the present and at the Last Glacial Maximum (LGM). Among 26 haplotypes, one was widely distributed, but most was restricted to either the eastern or western region. The populations with the highest levels of haplotype diversity were found in the Tianshan Mountains and its surroundings in the west, and the Helan Mountains and Alxa Plateau in the east. AMOVA and SAMOVA showed that over all populations, the species lacks phylogeographical structure, which is speculated to be the result of its specific biology. Neutrality tests and mismatch distribution analysis support past range expansions of the species. Comparing the current distribution to those cold and dry conditions in LGM, Z. xanthoxylon had a shrunken and more fragmented range during LGM. Based on the evidences from phylogeographical patterns, distribution of genetic variability, and paleodistribution modeling, Z. xanthoxylon is speculated most likely to have originated from the east and migrated westward via the Hexi Corridor.     

Phylogeography of the Macaronesian Lettuce Species <Emphasis Type="Italic">Lactuca watsoniana</Emphasis> and <Emphasis Type="Italic">L. palmensis</Emphasis> (Asteraceae)

The phylogenetic relationships and phylogeography of two relatively rare Macaronesian Lactuca species, Lactuca watsoniana (Azores) and L. palmensis (Canary Islands), were, until this date, unclear. Karyological information of the Azorean species was also unknown. For this study, a chromosome count was performed and L. watsoniana showed 2n = 34. A phylogenetic approach was used to clarify the relationships of the Azorean endemic L. watsoniana and the La Palma endemic L. palmensis within the subtribe Lactucinae. Maximum parsimony, Maximum likelihood and Bayesian analysis of a combined molecular dataset (ITS and four chloroplast DNA regions) and molecular clock analyses were performed with the Macaronesian Lactuca species, as well as a TCS haplotype network. The analyses revealed that L. watsoniana and L. palmensis belong to different subclades of the Lactuca clade. Lactuca watsoniana showed a strongly supported phylogenetic relationship with North American species, while L. palmensis was closely related to L. tenerrima and L. inermis, from Europe and Africa. Lactuca watsoniana showed four single-island haplotypes. A divergence time estimation of the Macaronesian lineages was used to examine island colonization pathways. Results obtained with BEAST suggest a divergence of L. palmensis and L. watsoniana clades c. 11 million years ago, L. watsoniana diverged from its North American sister species c. 3.8 million years ago and L. palmensis diverged from its sister L. tenerrima, c. 1.3 million years ago, probably originating from an African ancestral lineage which colonized the Canary Islands. Divergence analyses with *BEAST indicate a more recent divergence of the L. watsoniana crown, c. 0.9 million years ago. In the Azores colonization, in a stepping stone, east-to-west dispersal pattern, associated with geological events might explain the current distribution range of L. watsoniana.     

Genomic structure,expression and association study of the porcine <Emphasis Type="Italic">FSD2</Emphasis>

The fibronectin type III and SPRY domain containing 2 (FSD2) on porcine chromosome 7 is considered a candidate gene for pork quality, since its two domains, which were present in fibronectin and ryanodine receptor. The fibronectin type III and SPRY domains were first identified in fibronectin and ryanodine receptor, respectively, which are candidate genes for meat quality. The aim of this study was to elucidate the genomic structure of FSD2 and functions of single nucleotide polymorphisms (SNPs) within FSD2 that are related to meat quality in pigs. Using a bacterial artificial chromosome clone sequence, we revealed that porcine FSD2 consisted of 13 exons encoding 750 amino acids. In addition, FSD2 was expressed in heart, longissimus dorsi muscle, psoas muscle, and tendon among 23 kinds of porcine tissues tested. A total of ten SNPs, including four missense mutations, were identified in the exonic region of FSD2, and two major haplotypes were obtained based on the SNP genotypes of 633 Berkshire pigs. Both haplotypes were associated significantly with intramuscular fat content (IMF, P < 0.020) and moisture percentage (MP, P < 0.002). Moreover, haplotype 2 was associated with meat color, affecting yellowness (P = 0.002). These haplotype effects were further supported by the alteration of putative protein structures with amino acid substitutions. Taken together, our results suggest that FSD2 haplotypes are involved in regulating meat quality including IMF, MP, and meat color in pigs, and may be used as meaningful molecular makers to identify pigs with preferable pork quality.     

Evaluation of <Emphasis Type="Italic">ZmCCT</Emphasis> haplotypes for genetic improvement of maize hybrids

Key message

The elite ZmCCT haplotypes which have no transposable element in the promoter could enhance maize resistance to Gibberella stalk rot and improve yield-related traits, while having no or mild impact on flowering time. Therefore, they are expected to have great value in future maize breeding programs.

Abstract

A CCT domain-containing gene, ZmCCT, is involved in both photoperiod response and stalk rot resistance in maize. At least 15 haplotypes are present at the ZmCCT locus in maize germplasm, whereas only three of them are found in Chinese commercial maize hybrids. Here, we evaluated ZmCCT haplotypes for their potential application in corn breeding. Nine resistant ZmCCT haplotypes that have no CACTA-like transposable element in the promoter were introduced into seven elite maize inbred lines by marker-assisted backcrossing. The resultant 63 converted lines had 0.7-5.1 Mb of resistant ZmCCT donor segments with over 90% recovery rates. All converted lines tested exhibited enhanced resistance to maize stalk rot but varied in photoperiod sensitivity. There was a close correlation between the hybrids and their parental lines with respect to both resistance performance and photoperiod sensitivity. Furthermore, in a given hybrid A5302/83B28, resistant ZmCCT haplotype could largely improve yield-related traits, such as ear length and 100-kernel weight, resulting in enhanced grain yield. Of nine resistant ZmCCT haplotypes, haplotype H5 exhibited excellent performance for both flowering time and stalk rot resistance and is thus expected to have potential value in future maize breeding programs.

     

Heteroplasmy due to chloroplast paternal leakage: another insight into <Emphasis Type="Italic">Phragmites</Emphasis> haplotypic diversity in North America

Chloroplasts contain several copies of their DNA, and intra-individual haplotypic variation (heteroplasmy) is common in plants, but unexplored in the cosmopolitan genus Phragmites. The aims of this study were to assess if heteroplasmy due to paternal leakage of the chloroplast occurs in Phragmites and which new insights into the evolutionary history of Phragmites australis in North America can be identified from the heteroplasmic variation. Eight non-native P. australis haplotypes occur in North America and can interbreed with P. australis ssp. americanus and P. australis var. berlandieri, creating opportunities for biparental inheritance of distinctive haplotypes. The polymorphism in the trnT-trnL sequence length revealed seventeen cases of heteroplasmy worldwide, in contact zones of distantly related haplotypes and in known hybrid populations, nine of which occurred in North America. In America, the cloned sequences, combined with nuclear markers, identified recombined haplotypes between native P. australis ssp. americanus and invasive P. australis haplotype M, and between the species P. mauritianus and P. australis, due to chloroplast paternal leakage. The occurrence of heteroplasmy and recombined haplotypes suggest a local origin for some of the rare non-native haplotypes occurring in North America, and plastid leakage events in the evolutionary histories of P. australis ssp. americanus and P. australis var. berlandieri.