Codominant Markers Research Articles

Polypatex: an R package for paternity exclusion in autopolyploids.

Microsatellite markers have demonstrated their value for performing paternity exclusion and hence exploring mating patterns in plants and animals. Methodology is well established for diploid species, and several software packages exist for elucidating paternity in diploids; however, these issues are not so readily addressed in polyploids due to the increased complexity of the exclusion problem and a lack of available software. We introduce polypatex, an r package for paternity exclusion analysis using microsatellite data in autopolyploid, monoecious or dioecious/bisexual species with a ploidy of 4n, 6n or 8n. Given marker data for a set of offspring, their mothers and a set of candidate fathers, polypatex uses allele matching to exclude candidates whose marker alleles are incompatible with the alleles in each offspring-mother pair. polypatex can analyse marker data sets in which allele copy numbers are known (genotype data) or unknown (allelic phenotype data) - for data sets in which allele copy numbers are unknown, comparisons are made taking into account all possible genotypes that could arise from the compared allele sets. polypatex is a software tool that provides population geneticists with the ability to investigate the mating patterns of autopolyploids using paternity exclusion analysis on data from codominant markers having multiple alleles per locus.

Rhynchophorus palmarum in Disguise: Undescribed Polymorphism in the "Black" Palm Weevil.

During studies to adapt pheromone trapping of Rhynchophorus palmarum to the special coconut growing conditions at the Colombian Pacific coast, 152 atypically-colored specimens were captured in a total collection of 53,802 of the normally completely black weevil. Five specimens had the typical coloration of Rhynchophorus ferrugineus, an invasive species recently introduced to Aruba and Curação. A regional expansion of this invasion to the South American continent was feared and all atypical specimens were submitted to taxonomic analysis. Both conventional and molecular methods were employed. Conventional taxonomics confirmed the samples as belonging to R. palmarum but registered undescribed and species-atypical morphological variability in the subgular suture (wide vs. narrow), the ratio between intraocular distance and width of antennal scrobes (>0.35 vs. < 0.29) and the indentation of the mandibles (up to three mandibular teeth vs. bilobed). Molecular analysis placed all samples inspected, black and reddish alike, firmly within the R. palmarum group and the hypothesis of having inter-specific hybrids was rejected using co-dominant single sequence repeat markers with allelic specificity for both species.

Development and characterization of a co-dominant molecular marker via sequence analysis of a genomic region containing the Female (F) locus in cucumber (Cucumis sativus L.)

Cucumber is a typical monoecious having separate male and female flowers on the same plant, and sex expression in cucumber is mainly determined by three major genes: F/f, M/m and A/a. Gynoecy plays an important role in cucumber hybrid breeding, and the use of gynoecious lines as maternal parents ensures high productivity. This study aimed to identify a co-dominant marker linked to Female (F) locus to distinguish homozygous and heterozygous gynoecious lines for efficient selection of gynoecy in cucumber breeding. Firstly, we analyzed a 50-kb genomic sequence of five gynoecious and five monoecious inbred lines to detect the polymorphism linked to F locus. A pair of specific primers, Cs-BCAT-F/Cs-BCAT-R, based on an In/Del polymorphism at 3′-UTR of branched-chain amino acid transaminase (BCAT) gene was designed to examine the polymorphism in gynoecious and monoecious parents, their F1 hybrids and two F2 segregating populations. The PCR fragments amplified with Cs-BCAT-F/Cs-BCAT-R co-segregated with sexual phenotypes in the F2 populations, behaving as a co-dominant marker with two alleles: F (gynoecious) and f (monoecious). When we further verified the consistency of the co-dominant marker using additional 55 diverse inbred lines, it can explain ~90 % of accessions. Linkage analysis also showed that the gene which enhances the number of female flowers co-segregated with the co-dominant marker on the long arm of chromosome 6. This is the first report for the development of F locus-specific co-dominant marker which can distinguish perfectly homozygous and heterozygous gynoecious, and it could be used in marker-assisted selection in cucumber breeding.

Functional Codominant Marker for Selecting the Fw Gene Conferring Resistance to Fusarium Wilt Race 1 in Pea

ABSTRACTFusarium oxysporum f. sp. pisi (Fop) is a major soil‐borne pathogen and the causal agent of Fusarium wilt of pea (Pisum sativum L.), resulting in significant yield losses. Resistant cultivars have become the most effective method for controlling this fungal disease. The gene controlling resistance to F. oxysporum race 1 in pea, Fw, is located on linkage group (LG) III and widely used in breeding programs. Although this locus is routinely used for developing resistant cultivars, a robust codominant DNA marker for selection of the Fw gene is not currently available. We developed a breeder‐friendly functional codominant cleaved amplified polymorphic sequence (CAPS) marker, THO, which can be used in pea breeding programs for selection of resistance to F. oxysporum race 1. Using this marker, we were able to select pea lines with 96 to 98% accuracy in mapping populations and 94% accuracy in advanced pea breeding lines. This marker, in combination with other gene based markers (AnMtL6, Mt5_56, and PRX1TRAP13) developed from conserved sequences of closely related legume species, lays the foundation for candidate gene identification through comparative mapping.

Characterisation of cannabinoid composition in a diverse Cannabis sativa L. germplasm collection

AbstractThe ability to characterise cannabinoid chemical phenotype (chemotype) accurately is important for the development of Cannabissativa L. cultivars specific for pharmacological, hemp fibre, or seed end use. Although a number of chemotyping and genotyping methods have previously been developed to predict and characterise cannabinoid composition, only a subset of the gene pool has been examined. A representative survey from a wide range of geographically and genetically diverse C. sativa accessions using liquid chromatography–mass spectrometry (LC–MS) cannabinoid profiling together with dominant and co-dominant DNA marker assays was performed. Overall variability of chemotype across the gene pool was found to be three-fold greater within heterozygote genotypes than previously reported. Interestingly, an individual plant of East Asian origin was found to exhibit a rare propyl alkyl cannabinoid homologue and a chemotype inconsistent with the predicted genotype. We propose that in order to carry out comprehensive screening of genetic resource collections and to identify chemotypic variants specific for end-use pharmacological applications, a strategy which adopts both cannabinoid profiling and the co-dominant DNA marker assay is required. Further research with consideration of propyl-alkyl-cannabinoid homologues should explore the relationship between chemotype and genotype in greater detail.

Spore behaviors reveal a category of mating-competent infertile heterokaryons in the offspring of the medicinal fungus Agaricus subrufescens.

Strain breeding is much less advanced in the edible and medicinal species Agaricus subrufescens than in Agaricus bisporus, the button mushroom. Both species have a unifactorial system of sexual incompatibility, a mating type locus tightly linked to a centromere, and basidia producing both homokaryotic (n) and heterokaryotic (n + n) spores. In A. bisporus, breeding is mainly based on direct selection among the heterokaryotic offspring and on hybridization between homokaryotic offspring. The parental heterozygosity is highly maintained in the heterokaryotic offspring due to suppression of recombination and preferential pairing in the spores of nuclei, each one per second meiotic divisions; such "non-sister nuclei" heterokaryons are fertile. In A. subrufescens, recent studies revealed that recombination is not suppressed and that nuclei from the same second meiotic division can also be paired in a spore that give rise to a "sister nuclei" heterokaryon in which the nuclei bear the same mating type allele. The objective of the present work was to investigate the potential function of the different categories of spores in A. subrufescens and their possible use in a genetic breeding program. Using eight co-dominant molecular markers, we found that half of the offspring of the A. subrufescens strain WC837 were heterokaryotic, one quarter of them being sister nuclei heterokaryons. These heterokaryons were infertile and behaved like homokaryons, being even able to cross between each other. In contrast, non-sister nuclei heterokaryons could fruit but inconsistently due to inbreeding depression. Potential roles of these two categories of heterokaryons in nature and consequences for strain breeding are discussed.

Development and characterization of marker MBH1 simultaneously tagging genes Pm21 and PmV conferring resistance to powdery mildew in wheat

Wheat-Haynaldia villosa translocations T6V#2S.6AL and T6V#4S.6DL, carriers of Pm21 and PmV, respectively, continue to contribute powdery mildew resistance in wheat varieties in China. Based on colinearity between Brachypodium distachyon and Triticeae species, genomic sequences from gene intervals of B. distachyon physically linked to a homolog of Stpk-V, a key part of Pm21, were used to design primers and screen for codominant and stable markers. An anonymous marker, MBH1, tagging both Pm21 in 6V#2S and PmV in 6V#4S was identified. It also distinguished wheat 6AS- and 6DS-derived homoeoalleles of MBH1. Sequence length comparisons showed a decreasing order of 6AS > 6DS > 6V#2S > 6V#4S. F2 segregation analyses were conducted on crosses Yangmai 18 (T6V#2S.6AL)/Yangmai 19 and Yangmai 16/Yangmai 22 (T6V#4S.6DL). MBH1 detected homozygosity of both Pm21 and PmV in segregating populations. The results also showed that T6V#2S.6AL is more transmittable than T6V#4S.6DL. Using MBH1, we reconfirmed the identities of powdery mildew resistance genes in Yangmai 21, Zhenmai 9, and Yangmai 97G59. The resistance donor to all three was T6V#2S.6AL, indicating that the published pedigrees were not correct. Pm21 in NAU419-Y15, an intercalary translocation carrying Pm21, was also tagged by MBH1. MBH1 is a broadly applicable marker for selecting and distinguishing the translocation chromosomes carrying Pm21 and PmV, which continue to be effective in China.

Mapping of Pi, a gene conferring pink leaf in ornamental kale (Brassica oleracea L. var. acephala DC)

We previously found that pink leaf is conferred by a single semi-dominant gene in ornamental kale. To map this gene, we constructed an F2 segregating population containing 184 individuals by crossing W02–7, a white-leaved inbred line, with P02–9, a pink-leaved inbred line. We screened 297 simple sequence repeat (SSR) and 437 sequence-related amplified polymorphism (SRAP) markers using bulked segregant analysis. We identified one SSR and seven SRAP markers that linked tightly to the pink-leaf (Pi) gene. To obtain more specific genomic markers, we converted six SRAPs to sequence-characterized amplified region (SCAR) markers. We constructed a genetic linkage map of the Pi locus using one SSR and five SCAR markers, spanning a total interval of 15.0 cM. One SSR marker, Ni2C12, and one co-dominant SCAR marker, Boac04, flanked Pi on either side at distances of 0.6 and 2.4 cM, respectively. Based on the reference genome sequence of Brassica oleracea, we positioned Pi on the top of chromosome C3. We also detected that pink hypocotyl co-segregated with pink inner leaf. These markers provide the basis for fine-scale mapping and cloning of Pi, and may be used for marker-assisted selection in ornamental kale breeding programs.

Estimation of outcrossing rates in interspecific backcross plants of Jatropha curcas (L.) using AFLP and SSR markers.

In this paper, we report the estimates of outcrossing rates using open-pollinated progeny arrays of 40 BC1 individuals of Jatropha developed as a result of interspecific hybridization between J. curcas and J. integerrima. For analysis PCR-based dominant AFLP and codominant SSR markers were used. The multilocus outcrossing rate (tm) estimated from AFLP markers (0.892±0.112) are almost in the same range with SSR (0.884±0.293) markers which indicate a high level of heterozygosity. A low value of inbreeding coefficient (F) also points out to the fact that outcrossing was the prevalent mode of reproduction in Jatropha and suggests maintenance of adequate genetic variability within families.

Characterization of a Triticum aestivum–Dasypyrum villosum T2VS·2DL translocation line expressing a longer spike and more kernels traits

By using 2V-specific EST-PCR markers and sequential GISH/FISH analysis, we identified four homozygous CS-2V translocation lines, including a novel compensating T2VS·2DL translocation line NAU422. This translocation line has longer spikes and produces more grains per spike than its recurrent parent CS and three other translocation lines, which could be a valuable resource in wheat yield improvement. Dasypyrum villosum (2n=14, VV), the wild relative of wheat, possesses novel and superior alleles at many important loci and should be utilized to improve the genetic diversity of cultivated wheat and may be very helpful for the improvement of wheat yield. In this study, four homozygous Chinese Spring (CS)-D. villosum translocation lines containing different fragments of chromosome 2V were characterized from a pool, including 76 translocations that occur in chromosomes 1V through 7V of D. villosum by both molecular markers and cytogenetic analysis. A rough physical map of 2V was developed which included nine markers in three segments of the short arm and ten markers in the long arm. The photoperiod response gene of D. villosum (Ppd-V1) was physically mapped to the FL 0.33-0.53 region of 2VS, while the gene controlling bristles on the glume ridges (Bgr-V1) was mapped to 2VS FL 0.00-0.33. A novel compensating Triticum aestivum-D. villosum Robertsonian translocation line T2VS·2DL (NAU422) with good plant vigor and full fertility was further characterized by sequential genomic in situ hybridization and fluorescent in situ hybridization and the use of molecular markers. Compared to its recurrent parent CS and three other translocation lines, the T2VS·2DL translocation line has longer spikes, more spikelets and more grains per spike in two season years, which suggested that the alien segment may carry yield-related genes of D. villosum. The developed T2VS·2DL translocation line with its morphological and co-dominant molecular markers could be utilized as a novel germplasm for high-yield wheat breeding.

Development of genome-wide insertion/deletion markers in rice based on graphic pipeline platform.

DNA markers play important roles in plant breeding and genetics. The Insertion/Deletion (InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and labor-intensive. We developed an end-to-end computational solution (InDel Markers Development Platform, IMDP) to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequences alignment pipeline (AGA-pipe) and next-generation re-sequencing data mapping pipeline (NGS-pipe). With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGA-pipe and NGS-pipe, we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction (PCR) analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, to make them available to the public, we have integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, http://202.120.45.71/). The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

Development of a diagnostic co-dominant marker for stem rust resistance gene Sr47 introgressed from Aegilops speltoides into durum wheat.

A robust and diagnostic STS marker for stem rust resistance gene Sr47 was developed and validated for marker-assisted selection. Stem rust (caused by Puccinia graminis f. sp. tritici, Pgt) resistance gene Sr47, originally transferred from Aegilops speltoides to durum wheat (Triticum turgidum subsp. durum) line DAS15, confers a high level of resistance to Pgt race TTKSK (Ug99). Recently, the durum Rusty 5D(5B) substitution line was used to reduce the Ae. speltoides segment, and the resulting lines had Sr47 on small Ae. speltoides segments on wheat chromosome arm 2BL. The objective of this study was to develop a robust marker for marker-assisted selection of Sr47. A 200-kb segment of the Brachypodium distachyon genome syntenic with the Sr47 region was used to identify wheat expressed sequence tags (ESTs) homologous to the B. distachyon genes. The wheat EST sequences were then used to develop sequence-tagged site (STS) markers. By analyzing the markers for polymorphism between Rusty and DAS15, we identified a co-dominant STS marker, designated as Xrwgs38, which amplified 175 and 187bp fragments from wheat chromosome 2B and Ae. speltoides chromosome 2S segments, respectively. The marker co-segregated with the Ae. speltoides segments carrying Sr47 in the families from four BC2F1 plants, including the parent plants for durum lines RWG35 and RWG36 with the pedigree of Rusty/3/Rusty 5D(5B)/DAS15//47-1 5D(5B). Analysis of 62 durum and common wheat cultivars/lines lacking the Sr47 segment indicated that they all possessed the 175-bp allele of Xrwgs38, indicating that it was diagnostic for the small Ae. speltoides segment carrying Sr47. This study demonstrated that Xrwgs38 will facilitate the selection of Sr47 in durum and common wheat breeding.

Characterization of recombinants of the Aegilops peregrina-derived Lr59 translocation of common wheat.

A compensating, recombined Lr59 translocation with greatly reduced alien chromatin was identified. Microsatellite locus Xdupw217 occurs within the remaining segment and can be used as a co-dominant marker for Lr59. In earlier studies, leaf rust (caused by Puccinia triticina Eriks.) resistance gene Lr59 was transferred from Aegilops peregrina (Hackel) Maire et Weiler to chromosome arm 1AL of common wheat (Triticum aestivum L.). The resistance gene was then genetically mapped on the translocated chromosome segment following homoeologous pairing induction. Eight recombinants that retained the least alien chromatin apparently resulted from crossover within a terminal region of the translocation that was structurally different from 1AL. These recombinants could not be differentiated by size, and it was not clear whether they were compensating in nature. The present study determined that the distal part of the original translocation has group 6 chromosome homoeology and a 6BS telomere (with the constitution of the full translocation chromosome being 1AS·1L(P)·6S(P) ·6BS). During the allosyndetic pairing induction experiment to map and shorten the full size translocation, a low frequency of quadrivalents involving 1A, the 1A translocation, and two 6B chromosomes was likely formed. Crossover within such quadrivalents apparently produced comparatively small compensating alien chromatin inserts within the 6BS satellite region on chromosome 6B of seven of the eight recombinants. It appears that the Gli-B2 storage protein locus on 6BS has not been affected by the recombination events, and the translocations are therefore not expected to affect baking quality. Simple sequence repeat marker results showed that Lr59-151 is the shortest recombinant, and it will therefore be used in breeding. Marker DUPW217 detects a homoeo-allele within the remaining alien chromatin that can be used for marker-assisted selection of Lr59.

Development of a SCAR marker linked to bacterial wilt (Ralstonia solanacearum) resistance in tomato line Hawaii 7996 using bulked-segregant analysis

We report the development of a codominant sequence characterized amplified region (SCAR) marker linked to bacterial wilt resistance in tomato line Hawaii 7996. Bulked segregant analysis was employed for rapid identification of RAPD markers linked to resistance genes. Genomic DNA from six resistant F9 recombinant inbred lines (RILs) and six susceptible F9 RILs, which derived from a cross between S. lycopersicum Hawaii 7996 (resistant parent) and S. pimpinellifolium WVa 700 (susceptible parent) were pooled in to an R-pool and an S-pool, respectively. A total of 800 RAPD primers were screened and only six primers (UBC#176, 205, 287, 317, 350, and 676) showed polymorphism between R- and S- pools. Of these, only two markers UBC#176 and 317 revealed a 100% linkage in the individual plants comprising the contrasting bulks. Of these, the marker UBC#176 was converted into a codominant SCAR marker and designated as SCU176-534. The marker SCU176-534 was confirmed by genotyping the individual of the R- and S- pools and gave the same result as UBC#176. When the marker SCU176-534 was further validated for association with resistance and its potential for maker-assisted selection (MAS) in 92 tomato lines and cultivars, the results showed that none of these carries the resistance gene. Thus, SCAR marker SCU176-534 can be used in early selection of resistant lines when Hawaii 7996 is used as a parent in a breeding program.

Genetic identity of common buckwheat (Fagopyrum esculentum Moench) landraces locally cultivated in the Alps

The conservation of landraces in Europe is challenging because very often they have already disappeared or cannot be properly identified, which in turn prevents any possibility for their utilization. This work deals with the collection of molecular and historical data to identify and study the original landraces of common buckwheat (Fagopyrum esculentum Moench), locally cultivated in Northern Italy (Valtellina) and to date surviving among other commercial varieties, recently introduced in the same areas of the Alps. As plant materials of F. esculentum, we analyzed a number of Italian accessions along with two foreign accessions from Poland and Nepal, for a total of 174 individuals. Molecular investigations were based on a set of eight nuclear SSR marker loci. The mean observed heterozygosity over all accessions was equal to Ho = 0.466, being significantly lower than the expected heterozygosity (He = 0.764). A major finding was the recognition of a marked inbreeding rate (Fit = 0.387) and a reduced fixation index (Fst = 0.061), indicating that most genetic variation is found within populations. A significant overall gene flow among accessions was found (Nm = 3.846). Results indicated that only two of the examined accessions, the so-called “Nustran” and “Curunin”, could be considered, authentic Valtellina landraces. On the basis of results, we successfully developed a multi-locus marker system and identified a number of co-dominant marker alleles suitable for genetic traceability and authenticity certification of a “Nustran” and a “Curunin” autochthonous landraces of Valtellina and its food derivatives (i.e., Pizzoccheri, Polenta taragna).

Development of a SNP-based CAPS assay for the Me1 gene conferring resistance to root knot nematode in pepper

Root knot nematodes (Meloidogyne spp.) are significant agricultural pests on many crops, including pepper (Capsicum annuum). Host plant resistance offers the most sustainable means of controlling this pest. A cluster of genes on chromosome 9 confers resistance, with Me1 providing protection against three nematode species: M. incognita, M. javanica and M. arenaria. We describe the development of a codominant CAPS marker located 1.13 cM away from the Me1 gene. This marker should be useful for marker assisted selection of nematode resistance in pepper breeding programs.

Development of co-dominant SCAR markers linked to resistant gene against the Fusarium oxysporum f. sp. radicis-lycopersici.

We developed highly reliable co-dominant SCAR markers linked to the Frl gene. FORL testing is difficult. The marker is expected to be quickly adapted for MAS by tomato breeders. Fusarium oxysporum f. sp. radicis-lycopersici causes Fusarium crown and root rot (FCR), an economically important soil-borne disease of tomato. The resistance against FCR is conferred by a single dominant gene (Frl) located on chromosome 9. The aim of this study was to develop molecular markers linked to the Frl gene for use in marker-assisted breeding (MAS) programs. The FCR-resistant 'Fla. 7781' and susceptible 'B560' lines were crossed, and F1 was both selfed and backcrossed to 'B560' to generate segregating F2 and BC1 populations. The two conserved set II (COSII) markers were found linked to the Frl gene, one co-segregated with FCR resistance in both F2 and BC1 populations and the other was 8.5 cM away. Both COSII markers were converted into co-dominant SCAR markers. SCARFrl marker produced a 950 and a 1000 bp fragments for resistant and susceptible alleles, respectively. The linkage of SCARFrl marker was confirmed in BC2F3 populations developed by backcrossing the resistant 'Fla. 7781' to five different susceptible lines. The SCARFrl marker has been in use in the tomato breeding programs in BATEM, Antalya, Turkey, since 2012 and has proved highly reliable. The SCARFrl marker is expected to aid in the development of FCR-resistant lines via marker-assisted selection (MAS).

Sequence-characterized amplified polymorphism markers for selecting rind stripe pattern in watermelon (Citrullus lanatus L.)

The inheritance of foreground stripe pattern in rind of watermelon fruits [Citrullus lanatus (Thunb.) Matsum. & Nakai] was evaluated and molecular markers for selecting the Jubilee-type (JT) stripe pattern were developed based on bulked segregant analysis (BSA). Divergence in rind pattern among F2 progeny derived from crossing Crimson-type (CT) ‘Arka Manik’ (AM) with JT ‘TS34’ (TS) indicated that stripe pattern is a quantitative trait controlled by more than one gene. The BSA of F2 plants (derived from a cross between ‘AM’ and ‘TS’) using 60 random amplified polymorphic DNA (RAPD) primers revealed a distinct RAPD band (AT14-900) polymorphic between ‘AM’ (CT) and ‘TS’ (JT). The AT14-900 sequence (925 bp) was blasted to the reference watermelon (97103) genome and high sequence similarity (97.8%) was identified on physical location of 26246077 to 26246993 bp on chromosome 6. Two expressed sequence tags (ESTs) designated ‘wsbin6-10’ and ‘wsbin6-11’ that were closely linked to AT14-900 on a genetic linkage map (developed using the F2 population derived from ‘AM’ x ‘TS’) were positioned 2,216 kb and 71 kb from AT14-900, respectively on the reference watermelon genome sequence. Marker genotyping of the F2 population showed that wsbin6-11 was tightly linked to the JT stripe pattern of ‘TS’ and could be a useful codominant marker for selecting this trait. In a test using 100 breeding lines, 34 of the 36 lines carrying the JT stripe pattern were homozygous for the wsbin6-11 marker (450 bp) derived from ‘TS’, while other lines (e.g., with no stripe or CT stripe pattern) were homozygous for the wsbin6-11 marker (420 bp) derived ‘AM’. These results indicated that wsbin6-11 would be a useful marker in watermelon breeding programs aiming to select for the JT stripe pattern from other various foreground and background rind patterns.

Assessment of Genetic Diversity of Argania spinosa L. Growing in Arid and Semi-arid Areas of Morocco as Revealed by Inter-Simple Sequence Repeats

Argania spinosa L. (Sapotaceae family), endemic to Morocco, is a multipurpose tree with an important ecological and socio-economical interest. Nevertheless, the sustainability of the agro-forestry system is now threatened by overgrazing and over-exploitation leading to an alarming decline in the number of trees. In the present study, inter-simple sequence repeats (ISSR) markers were used to evaluate the genetic variation and to assess the genetic diversity distribution within and among 17 argan populations growing naturally under semi-arid and arid climate. Thus, a total of seven primers generated 260 well-defined bands, with an average of 37.14 bands per primer. Studied populations showed a relatively high level of genetic diversity at species level and low level of genetic diversity at population level. The percentage of polymorphic bands, Nei's gene diversity and Shannon's information index at population and species level were 30.15%, 0.164, 0.217 and 98.8%, 0.172, 0.293, respectively. A relative low level of genetic differentiation (Gst = 0.39) was in agreement with the results obtained from the analysis of molecular variance (AMOVA). Estimated gene flow was Nm = 0.781 among populations. Mantel test revealed a non-significant correlation between genetic and geographic distance (r = 0.065, P < 0.05), suggesting that the geographic distribution is not the major factor that shaped the present population genetic structure. The results can help preserve A. spinosa L. tree as an endangered species, however, refining these finding using co-dominant markers is recommended in order to establish conservation strategies.

Opportunities of marker-assisted selection for rice fragrance through marker-trait association analysis of microsatellites and gene-based markers.

Developing fragrant rice through marker-assisted/aided selection (MAS) is an economical and profitable approach worldwide for the enrichment of an elite genetic background with a pleasant aroma. The PCR-based DNA markers that distinguish the alleles of major fragrance genes in rice have been synthesised to develop rice scent biofortification through MAS. Thus, the present study examined the aroma biofortification potential of these co-dominant markers in a germplasm panel of 189 F2 progeny developed from crosses between a non-aromatic variety (MR84) and a highly aromatic but low-yielding variety (MRQ74) to determine the most influential diagnostic markers for fragrance biofortification. The SSRs and functional DNA markers RM5633 (on chromosome 4), RM515, RM223, L06, NKSbad2, FMbadh2-E7, BADEX7-5, Aro7 and SCU015RM (on chromosome 8) were highly associated with the 2AP (2-acetyl-1-pyrroline) content across the population. The alleles traced via these markers were also in high linkage disequilibrium (R(2) > 0.70) and explained approximately 12.1, 27.05, 27.05, 27.05, 25.42, 25.42, 20.53, 20.43 and 20.18% of the total phenotypic variation observed for these biomarkers, respectively. F2 plants harbouring the favourable alleles of these effective markers produced higher levels of fragrance. Hence, these rice plants can be used as donor parents to increase the development of fragrance-biofortified tropical rice varieties adapted to growing conditions and consumer preferences, thus contributing to the global rice market.