A new aspect of genetic diversity of Indonesian oil palm (Elaeis guineensis Jacq.) revealed by isoenzyme and AFLP markers and its consequences for breeding

Oil palm (Elaeis guineensis Jacq.) plays an important economic role in some countries of Southeast Asia like Indonesia, which is the world’s second producer of palm and palm kernel oil. The quality improvement of planting material needs a better understanding of the genetic relationships between genotypes from different populations used in the breeding programmes. In this study, 48 parents, representative of four populations used in Indonesian Oil Palm Research Institute (IOPRI) breeding programmes, were analysed with five selected AFLP primer pairs and four isoenzymatic systems. One hundred and fifty eight scorable band levels were generated of which 96 (61%) were polymorphic. AFLP allowed us to identify off–type descendants which were excluded from analysis. The use of unbiased Rogers distance clearly separated the four studied populations. The Neighbor-Joining method re-groups two African populations which are known as originating from different regions. Nevertheless, the variability revealed is in accordance with oil palm breeders’ knowledge. The results obtained with AFLP showed that the crosses among the African sub-population, which is excluded in oil palm reciprocal recurrent selection (RRS) breeding programmes, may be more interesting than the crosses between the African and the Deli populations. Received: 9 August 1999 / Accepted: 28 February 2000     

Phenological stages and degree days of oil palm crosses grown under irrigation in tropical conditions

Studies on phenology and growing degree days (GDD) of four oil palm crosses, that is, Palode, Deli × Nigeria, United Plantations and Deli × Ghana were conducted in India under tropical conditions. Observations were recorded in adult oil palms over a period of 1.5 years from visual opening of spear leaf to development of female flower till harvest. Biologische Bundesantalt, Bundessortenamt and Chemische Industrie (BBCH) General Scale was used for conducting various phenological growth stages. The GDD from development of spear leaf to maturity in the different crosses varied between 6,320.2 and 6,937.3. The degree days and duration from development of spear leaf to maturity were less in the crosses of United Plantations. The time taken for spear leaf unfolding to maturity and flower opening to maturity in the different crosses, respectively, varied from 447.9 to 485.2 days and 145.8 to 153.7 days. The study gives an insight in evaluating thermal time for achieving various phenophases in oil palm and genotypic variations of time taken in attaining the different phenophases that have been documented. Climatic and yield prediction models can also be evolved through these studies.     

Prediction of oil palm (Elaeis guineensis, Jacq.) agronomic performances using the best linear unbiased predictor (BLUP)

Reciprocal recurrent selection (RRS) has been adopted for oil palm breeding in Indonesia.Due to a long selection cycle and the large area required, a satisfactory oil palm progeny trial is difficult to conduct.Knowledge of the parental genetic parametersis very important in achieving the expected genetic progress, but the evaluation of these parameters is constrained by highly unbalanced data sets. In this study, the unbalanced agronomic data sets and the pedigree information of an oil palm breeding programme in Indonesia were analysed by using the restricted maximum likelihood (REML) and the best linear unbiased predictor (BLUP)methods. The characters analysed were bunch and oil yields of the adult period (from 7 to 9 years after planting). The coefficients of parentage varied from 0.125 to 0.891 and from zero to 0.750 between parents in the Deli and African groups, respectively.The average coefficients of inbreeding were 0.269 and 0.166 for the parents within the Deli and African groups, respectively. The additive variances of the bunch number, industrial oil-extraction rate and oil yield characters were higher in the parents of the Deli group than those in the African ones. The coefficients of correlation between the predicted and observed hybrids performances varied from 0.55 to 0.64 for oil yield, 0.49 to 0.71 for bunch number, 0.47 to 0.58 for bunch production, 0.48 to 0.64 for industrial oil-extraction rate and 0.42 to 0.56 for plant-height increment. For selection on the basis of oil yield character, BLUPs ability to predict single-cross performance should be sufficient, and will result in a significant contribution to the oil palm seed and clone productions. Received: 3 January 2000 / Accepted: 3 July 2000     

Exploiting an oil palm EST database for the development of gene-derived SSR markers and their exploitation for assessment of genetic diversity

A total of 5,521 expressed sequence tags (ESTs) from oil palm were used to search for type and frequency of simple sequence repeat (SSR) markers. Dimeric repeat motifs appeared to be the most abundant, followed by tri-nucleotide repeats. Redundancy was eliminated in the original EST set, resulting in 145 SSRs in 136 unique ESTs (114 singletons and 22 clusters). Primers were designed for 94 (69.1%) of the unique ESTs (consisting of 14 consensus and 80 singletons). Primers for 10 EST-SSRs were developed and used to evaluate the genetic diversity of 76 accessions of oil palm originating from seven countries in Africa, and the standard Deli dura population. The average number of observed and effective alleles was 2.56 and 1.84, respectively. The EST-SSR markers were found to be polymorphic with a mean polymorphic information content value of 0.53. Genetic differentiation (F _ST) among the populations studied was 0.2492 indicating high level of genetic divergence. Moreover, the UPGMA (unweighted pair-group method with arithmetic mean) analysis revealed a strong association between genetic distance and geographic location of the populations studied. The germplasm materials exhibited higher diversity than Deli dura, indicating their potential usefulness in oil palm improvement programmes. The study also revealed that the populations from Nigeria, Congo and Cameroon showed the highest diversity among the germplasm evaluated in this study. The EST-SSRs further demonstrated their worth as a new source of polymorphic markers for phylogenetic analysis, since a high percentage of the markers showed transferability across species and palm taxa.     

Possible sources of genetic resistance in oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis> Jacq.) to basal stem rot caused by <Emphasis Type="Italic">Ganoderma boninense</Emphasis> – prospects for future breeding

Oil palm estates in southeast Asia suffer from substantial losses due to basal stem rot caused by Ganoderma boninense. Field observations have been carried out in North Sumatra, Indonesia, on a series of planting materials of known origin. Differences in susceptibility to the disease have been detected within the two Elaeis species, guineensis and oleifera. Within Elaeis guineensis, material of Deli origin is highly susceptible compared to material of African origin. It is also possible to detect differences in reaction between parents and between crosses within a given origin. The variability of resistance to basal stem rot within the same cross is also illustrated by the diverse responses of clones derived from palms of the same origin. The prospects opened up by these results are discussed, and the importance of performing an early selection test is highlighted.     

Microsatellite Analysis of Oil Palms and their Progenies Bred in Papua New Guinea

Our aim was to assess parental and population genetic variability in a partially nested set of breeding populations from the breeding program at Dami Research Station (West New Britain, PNG). Twenty microsatellite markers were tested for their ability to characterize genetic variation in oil palm populations bred at Dami Research Station. One hundred and twenty six individuals, including 100 F₁ tenera hybrids of Dami Deli crossed with either AVROS, Ghana or AVROS/Ghana breeding lines were analysed. Eighteen of these markers were polymorphic within and among populations, amplifying 103 alleles in oil palm. Three individuals of other palm species (Cocos nucifera and two Phoenix spp.) were included as outliers. With these markers we have the power to distinguish individual palms, hence we conclude that they will facilitate association of markers with important phenotypic traits to streamline future breeding and selection.     

Natural adaptation and human selection of northeast African sheep genomes

African sheep manifest diverse but distinct physio-anatomical traits, which are the outcomes of natural- and human-driven selection. Here, we generated 34.8 million variants from 150 indigenous northeast African sheep genomes sequenced at an average depth of ～54× for 130 samples (Ethiopia, Libya) and ～20× for 20 samples (Sudan). These represented sheep from diverse environments, tail morphology and post-Neolithic introductions to Africa. Phylogenetic and model-based admixture analysis provided evidence of four genetic groups corresponding to altitudinal geographic origins, tail morphotypes and possible historical introduction and dispersal of the species into and across the continent. Running admixture at higher levels of K (6 ≤ K ≤ 25), revealed cryptic levels of genome intermixing as well as distinct genetic backgrounds in some populations. Comparative genomic analysis identified targets of selection that spanned conserved haplotype structures overlapping clusters of genes and gene families. These were related to hypoxia responses, ear morphology, caudal vertebrae and tail skeleton length, and tail fat-depot structures. Our findings provide novel insights underpinning morphological variation and response to human-driven selection and environmental adaptation in African indigenous sheep.     

The genetics of rust resistance in sugar cane seedling populations

The inheritance of rust resistance was studied in sugar cane seedling populations using a factorial mating design over 1 summer and 2 winter seasons. Frequency distributions for rust infection pooled over 2 winter seasons for resistant x resistant parents were highly skewed with the majority of progenies grouped towards the resistant classes, whereas crosses between susceptible x highly susceptible parents tended to be skewed with the majority of progenies grouped towards the susceptible ones. Both categories of crosses produced transgressive segregants at either extremes. Distribution of infection within progeny of the selfed resistant parent ’R 570’ and distribution in the majority of crosses tended to support the hypothesis of a major gene with a dominant effect for resistance. However, the action of other minor genes acting in a quantitative way is also suggested. The female (F) and male (M) variance components were very important, and F×M interaction indicated the existence of non-additive genetic effects. F×S, M×S and F×M×S interaction mean squares were generally low or insignificant. Broad-sense heritability for the individual season ratings and for the combined ratings was high (0.75–0.90), whereas narrow-sense heritability was generally moderate (0.40–0.52) with the additive genetic effects accounting for 44–68% of the total genetic variation. The implications of these findings in the breeding for rust resistance in the local programme are discussed. Received: 2 June 1999 / Accepted: 22 June 1999     

Genetic diversity of oil palm (<Emphasis Type="Italic">Elaeis guineensis</Emphasis> Jacq.) germplasm collections from Africa: implications for improvement and conservation of genetic resources

A total of 723 accessions of oil palm (Elaeis guineensis Jacq.) from 26 populations representing ten countries in Africa and one Deli dura family were screened for allelic variation at seven enzyme loci from six enzyme systems using starch gel electrophoresis. On average, 54.5% of the loci were polymorphic (0.99 criterion). The average and effective number of alleles per locus was 1.80 and 1.35, respectively. Mean expected heterozygosity was 0.184, with values ranging from 0.109 (population 8, Senegal) to 0.261 (population 29, Cameroon). The genetic differentiation among populations was high (F_ST=0.301), indicating high genetic divergence. The calculation of F_ST by geographic zones revealed that the high F_ST was largely due to F_ST among populations in West Africa, suggesting diversifying selection in this region. The mean genetic distance across populations was 0.113. The lowest genetic distance (D) was observed between population 5 from Tanzania and population 7 from the Democratic Republic of the Congo (0.000) and the highest was found between population 4 from Madagascar and population 13 from Sierra Leone (0.568). The total gene flow across oil palm populations was low, with an Nm of 0.576, enhancing genetic structuring, as evident from the high F_ST values. UPGMA cluster analysis revealed three main clusters; the western outlying populations from Senegal and Sierra Leone were in one cluster but separated into two distinct sub-clusters; the eastern outlying populations from Madagascar were in one cluster; the populations from Angola, Cameroon, The Democratic Republic of the Congo, Ghana, Tanzania, Nigeria and Guinea were in one cluster. The Deli dura family seems to be closely related to population 6 from Guinea. Oil palm populations with high genetic diversity—i.e. all of the populations from Nigeria, Cameroon and Sierra Leone, population 6 of Guinea, population 1 of Madagascar and population 2 of Senegal should be used in improvement programmes, whereas for conservation purposes, oil palm populations with high allelic diversity (A_e), which include populations 22 and 29 from Cameroon, populations 39 and 45 from Nigeria, population 6 from Guinea, populations 5 and 13 from Sierra Leone and population 1 from Madagascar should be selected for capturing as much genetic variation as possible.Communicated by D.B. Neale     

Development and application of microsatellite markers for genomic analysis of papaya

Papaya has a relatively small genome, displays high levels of phenotypic diversity, and is amenable to transformation, making it attractive as a fruit tree model system. The high level of phenotypic diversity seen among papaya cultivars in the field does not correlate with the low levels of genotypic polymorphism thus far elucidated. The highly mutable nature of microsatellites or simple sequence repeats (SSRs) make them potentially powerful markers for distinguishing deoxyribonucleic acid (DNA) polymorphisms between closely related genotypes. Genomic research for papaya has resulted in a significant quantity of sequence data. We mined 28.1 Mb of bacterial artificial chromosomes end sequences, 5.8 Mb of complementary DNA, and 1.6 Mb of random genomic sequences for SSRs. We generated 938 SSR markers and tested for polymorphism among seven varieties that had been used to produce five mapping populations. The level of polymorphism was highest for Kaek Dum × 2H94 with 210 markers, followed by UH928 × SunUp with 194, AU9 × SunUp with 189, UH918 × SunUp with 177, and Kapoho × SunUp displaying the lowest level with 97. Variation in levels of polymorphism, motif predominance, and motif length between the genomic and genic fractions indicated differential selection pressures acting on the microsatellites in these two fractions. The microsatellites developed in this study will greatly assist in the genetic and physical mapping of the papaya genome as well as enhance breeders’ ability to improve the crop. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Temporal changes in allele frequencies in two European F2 flint maize populations under modified recurrent full-sib selection

Selection and random genetic drift are the two main forces affecting the selection response of recurrent selection (RS) programs by changes in allele frequencies. Therefore, detailed knowledge on allele frequency changes attributable to these forces is of fundamental importance for assessing RS programs. The objectives of our study were to (1) estimate the number, position, and genetic effect of quantitative trait loci (QTL) for selection index and its components in the base populations, (2) determine changes in allele frequencies of QTL regions due to the effects of random genetic drift and selection, and (3) predict allele frequency changes by using QTL results and compare these predictions with observed values. We performed QTL analyses, based on restriction fragment length polymorphisms (RFLPs) and simple sequence repeats (SSRs), in 274 F_2:3 lines of cross KW1265 × D146 (A × B) and 133 F_3:4 lines of cross D145 × KW1292 (C × D) originating from two European flint maize populations. Four (A × B) and seven (C × D) cycles of RS were analyzed with SSRs for significant allele frequency changes due to selection. Several QTL regions for selection index were detected with simple and composite interval mapping. In some of them, flanking markers showed a significant allele frequency change after the first and the final selection cycles. The correlation between observed and predicted allele frequencies was significant only in A × B. We attribute these observations mainly to (1) the high dependence of the power of QTL detection on the population size and (2) the occurrence of undetectable QTL in repulsion phase. Assessment of allele frequency changes in RS programs can be used to detect marker alleles linked to QTL regions under selection pressure. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Mapping QTL for leaf area in oil palm using genotyping by sequencing

Leaf area is an important parameter in oil palm breeding as it is positively correlated with oil yield. However, measurement of leaf area is tedious and also destructive. In the present study, a breeding population with 145 palms derived from a cross between Deli Dura and Avros Pisifera was used to construct a high-density linkage map and identify quantitative trait loci (QTL) for leaf area in oil palm. Using genotyping by sequencing, a linkage map containing 2413 SNPs was constructed. The total length of the linkage map was 1161.89 cM, with an average marker spacing of 0.48 cM. Based on the continuous phenotyping of leaf area from 2010 to 2015, two suggestive QTL for leaf area were mapped on chromosomes (Chr) 3 and 9. The allelic effects of the QTL associated with leaf area in the mapping population were estimated by linear regression using ordinary least squares method. The QTL on Chr 9 explained 13.3% of phenotypic variation for leaf area. A candidate gene, ARC5, within the narrow interval of QTL on Chr 9 was identified. The gene was significantly higher expressed in leaf than root and fruit of oil palm. This high-quality and SNP-based map supplies a base to fine map QTL for agronomic traits in oil palm, and the markers closely linked to the stable QTL may be used in marker-assisted selection in oil palm breeding.     

PLOIDAL CHANGES IN CLONAL CULTURES OF SPIROGYRA COMMUNIS AND IMPLICATIONS FOR SPECIES DEFINITION

A clonal culture of Spirogyra filaments of initially uniform width produced filaments of three additional significantly different widths. Group I filaments of the original clone were 30.9 ± 0.7 μm wide (mean ± SD, N = 50). Group I filaments produced Group II filaments (22.0 ± 1.1 μm) through vegetative growth and sexual reproduction. Zygospores from homothallic Group I filaments produced germlings representative of Groups I and II; zygospores from homothallic Group II filaments produced germlings representative of Group II only. Germlings of Groups III (27.7 ± 1.0 μm) and IV (44.9 ± 0.8 μm) were produced in the cross of I × II. Viable zygospores from homothallic Group III filaments were obtained. Cells of Group IV filaments were initially binucleate and did not conjugate. Of the six intergroup crosses possible, four resulted in conjugation-tube formation only; two crosses yielded zygospores (I × II and III × IV). Germlings from the successful cross of Groups III and IV produced filaments of all four groups. Chromosome counts were: Group I (24), Group II (12), Group III (18), and Group IV (24, one nucleus). Relative nuclear fluorescence values of mithramycin-stained DNA were (mean ± SD, N ≥ 30): Group I (11.1 ± 1.4), Group II (5.7 ± 0.7), Group III (8.8 ± 1.3), and Group IV (10.0 ± 0.9, one nucleus). Cytologically, Group II appears to be a diploid (2x), Group I a tetraploid (4x), and Group III a triploid (3x). Systematically, Groups I, II, and III key out to Spirogyra singularis, S. communis, and S. fragilis, respectively, using Transeau's mongraph of the family Zygnemataceae. These species are interpreted to represent a species complex of S. communis (whose name has priority) with the ancestral haploid (x = 6) missing.     

Rust mite resistance in apple assessed by quantitative trait loci analysis

The aim of this study was to assess the genetic basis of rust mite (Aculus schlechtendali) resistance in apple (Malus × domestica). A. schlechtendali infestation of apple trees has increased as a consequence of reduced side effects of modern fungicides on rust mites. An analysis of quantitative trait loci (QTLs) was carried out using linkage map data available for F₁ progeny plants of the cultivars ‘Fiesta’ × ‘Discovery’. Apple trees representing 160 different genotypes were surveyed for rust mite infestation, each at three different sites in two consecutive years. The distribution of rust mites on the individual apple genotypes was aggregated and significantly affected by apple genotype and site. We identified two QTLs for A. schlechtendali resistance on linkage group 7 of ‘Fiesta’. The AFLP marker E35M42-0146 (20.2 cM) and the RAPD marker AE10-400 (45.8 cM) were closest positioned to the QTLs and explained between 11.0% and 16.6% of the phenotypic variability. Additionally, putative QTLs on the ‘Discovery’ chromosomes 4, 5 and 8 were detected. The SSR marker Hi03a10 identified to be associated to one of the QTLs (AFLP marker E35M42-0146) was traced back in the ‘Fiesta’ pedigree to the apple cultivar ‘Wagener’. This marker may facilitate the breeding of resistant apple cultivars by marker assisted selection. Furthermore, the genetic background of rust mite resistance in existing cultivars can be evaluated by testing them for the identified SSR marker. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Post-zygotic gametic selection due to endosperm balance number explains unusual chromosome numbers of 3×× 2× progeny in Solanum

 Crosses between triploid and diploid genotypes are usually the best sources of trisomics in potato as well as in several other crop species. However, 3×× 2× crosses between triploid (2n=3×=36; 2EBN) Solanum commersonii-S. tuberosum hybrids and diploid (2n= 2×=24; 2EBN) genotypes gave progenies with a high number of extra chromosomes, 29–36, suggesting that only eggs with 17–24 chromosomes produced embryos that reached full development. Our hypothesis is that although triploids produce eggs with a range of chromosome numbers, 3×× 2× crosses involving a 2×(2EBN) parent favor eggs with a high chromosome number. These eggs have higher probabilities of possessing the same endosperm balance number (EBN) value (i.e. 1) of gametes produced by the 2EBN diploid parent to give the required 2:1 maternal to paternal EBN ratio in the hybrid endosperm. Under this model, trisomics are produced only if the diploid parent has an EBN of 1. Based on our results and those reported in the literature, it is proposed that in 3×(2EBN) × 2×(2EBN) crosses the endosperm balance number exercises negative selection for gametes with a low chromosome number, and a corresponding low EBN, and positive selection for gametes with a high chromosome number and EBN. Received: 2 April 1998 / Revision accepted: 27 October 1998     

QTL detection by multi-parent linkage mapping in oil palm (Elaeis guineensis Jacq.)

A quantitative trait locus (QTL) analysis designed for a multi-parent population was carried out and tested in oil palm (Elaeis guineensis Jacq.), which is a diploid cross-fertilising perennial species. A new extension of the MCQTL package was especially designed for crosses between heterozygous parents. The algorithm, which is now available for any allogamous species, was used to perform and compare two types of QTL search for small size families, within-family analysis and across-family analysis, using data from a 2 × 2 complete factorial mating experiment involving four parents from three selected gene pools. A consensus genetic map of the factorial design was produced using 251 microsatellite loci, the locus of the Sh major gene controlling fruit shell presence, and an AFLP marker of that gene. A set of 76 QTLs involved in 24 quantitative phenotypic traits was identified. A comparison of the QTL detection results showed that the across-family analysis proved to be efficient due to the interconnected families, but the family size issue is just partially solved. The identification of QTL markers for small progeny numbers and for marker-assisted selection strategies is discussed.     

Genomic regions involved in productivity of two interspecific poplar families in Europe. 1. Stem height, circumference and volume

Interspecific hybrids of Populus species are known for their superior growth. In this study, we examined the effect of the genetic background and contrasting environmental conditions on growth and searched for quantitative trait loci (QTL) affecting growth traits. To this end, two hybrid poplar families resulting from controlled crosses, Populus deltoides ‘S9-2’ × P. nigra ‘Ghoy’ (D × N, 180 F₁) and P. deltoides ‘S9-2’ × P. trichocarpa ‘V24’ (D × T, 182 F₁), were grown at two contrasting sites, Northern Italy and Central France. At the end of the second growing season, tree dimensions (stem height, circumference, and volume) were assessed. The performances of both families significantly differed within and between sites. Tree volume was significantly larger at the Italian site as compared to the French site. Genotype by environment interactions were significant but low for both families and for all growth traits. Tight correlations among the individual growth traits indicated that there may be a common genetic mechanism with pleiotropic effects on these growth traits. In line with previous studies, linkage groups I, VII, IX, X, XVI, XVII, and XIX appeared to have genomic regions with the largest effects on growth traits. This study revealed that (1) both families have high potential for selection of superior poplar hybrids due to the pronounced heterosis (hybrid vigor) and the large genetic variability in terms of growth and (2) the choice of site is crucial for poplar cultivation. Dillen and Storme contributed equally to the work. An erratum to this article can be found at     

Inheritance of reduced linolenic acid content in soybean seed oil

 Linolenic acid is the unstable component of soybean [Glycine max (L.) Merr.] oil that is responsible for the undesirable odors and flavors commonly associated with poor oil quality. Two mutants, M-5 and KL-8, have been identified that have lower linolenic acid levels in the seed oil than the ‘Bay’ cultivar. Our objective was to determine the relationships between the genetic systems controlling linolenic acid in these mutants. Reciprocal crosses were made between the mutants and ‘Bay’, and between the two mutants. No maternal effect for linolenic acid content was observed from the analysis of F₁ seeds in any of the crosses. The data for linolenic acid content in F₂ seeds of M-5בBay’ and KL-8בBay’ crosses satisfactorily fit a 1 : 2 : 1 and 3 : 1 ratio, respectively. For the M-5×KL-8 cross, segregation observed from the analysis of F₂ seeds for linolenic acid content satisfactorily fit a ratio of 3 more than either mutant: 12 within the range of the two mutants: 1 less than either mutant. The segregation ratio of F₂ seeds and the segregation of F₃ seeds from F₂ plants indicated that M-5 and KL-8 have alleles at different loci that control linolenic acid content. The allele in KL-8 has been designated as fanx (KL-8) to distinguish it from fan (M-5). The low linolenic acid segregates with the genotype fanfanfanxfanx provide additional germplasm to reduce the linolenic acid content from the seed oil of soybean. Received: 18 December 1995 / Accepted: 12 July 1996     

High density SNP and SSR-based genetic maps of two independent oil palm hybrids

Background

Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest.

Results

A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed.

Conclusions

The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-309) contains supplementary material, which is available to authorized users.     

A genetic linkage map for an apricot (<Emphasis Type="Italic">Prunus armeniaca</Emphasis> L.) BC<Subscript>1</Subscript> population mapping <Emphasis Type="Italic">plum pox virus</Emphasis> resistance

Plum pox virus (sharka; PPV) can cause severe crop loss in economically important Prunus species such as peach, plum, apricot, and cherry. Of these species, certain apricot cultivars (‘Stark Early Orange’, ‘Goldrich’, ‘Harlayne’) display significant levels of resistance to the disease and are the genetic substrate for studies of several xlaboratories working cooperatively to genetically characterize and mark the resistance locus or loci for marker-assisted breeding. The goals of the work presented in this communication are the characterization of the genetics of PPV resistance in ‘Stark Early Orange’ and the development of co-dominant molecular markers for marker-assisted selection (MAS) in PPV resistance breeding. We present the first genetic linkage map for an apricot backcross population of ‘Stark Early Orange’ and the susceptible cultivar ‘Vestar’ that segregates for resistance to PPV. This map is comprised of 357 loci (330 amplified fragment length polymorphisms (AFLPs), 26 simple sequence repeats (SSRs), and 1 morphological marker for PPV resistance) assigned to eight linkage groups. Twenty-two of the mapped SSRs are shared in common with genetic reference map for Prunus (T × E; Joobeur et al. 1998) and anchor our apricot map to the general Prunus map. A PPV resistance locus was mapped in linkage group 1 and four AFLP markers segregating with the PPV resistance trait, identified through bulk segregant analysis, facilitated the development of SSRs in this region. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Lalli, D.A. and Salava, J. contributed equally to this work.