Co-dominant Simple Sequence Repeat Research Articles

Registration of eight germplasm lines of upland cotton (Gossypium hirsutum L.) resistant to reniform nematodes (Rotylenchulus reniformis) with elite agronomic performance

AbstractCotton (Gossypium hirsutum L.) germplasm lines BARBREN‐713‐8 (Reg. no. GP‐1138, PI 701080), BARBREN‐713‐11 (Reg. no. GP‐1131, PI 701073), BARBREN‐713‐13 (Reg. no. GP‐1132, PI 701074), BARBREN‐713‐25 (Reg. no. GP‐1133, PI 701075), BARBREN‐713‐32 (Reg. no. GP‐1134, PI 701076), BARBREN‐713‐33 (Reg. no. GP‐1135, PI 701077), BARBREN‐713‐41 (Reg. no. GP‐1136, PI 701078), and BARBREN‐713‐48 (Reg. no. GP‐1137, PI 701079) were developed and released by the USDA‐ARS, Texas A&M AgriLife Research, and Cotton Incorporated in 2014. The objective of the release was to provide breeders with agronomically elite germplasm that is resistant to reniform nematode (Rotylenchulus reniformis). Four lines (BARBREN‐713‐8, ‐32, ‐33, and ‐48) also have simple sequence repeat (SSR) DNA markers for the Mi‐1 or Mi‐2 gene for resistance to root‐knot nematode [Meloidogyne incognita (Kolfoid & White) Chitwood]. The lines have excellent seedling vigor in fields infested with both nematodes and fungal root‐rot pathogens. Resistance to reniform nematode was transferred from G. barbadense GB713 (PI 608139) and is associated primarily with the Ren2GB713 gene on chromosome 21. This gene could be detected with the codominant SSR marker BNL3279_105 or the single nucleotide polymorphism marker GI‐187401. In controlled environment assays, these lines reported here suppressed numbers of reniform nematode eggs by 74–92% compared with ‘FiberMax FM966’. The lines outyielded and had fiber quality equal to or greater than several commercial cultivars.

Creation of New Oregano Genotypes with Different Terpene Chemotypes via Inter- and Intraspecific Hybridization.

Oregano is a medicinal and aromatic plant of value in the pharmaceutical, food, feed additive, and cosmetic industries. Oregano breeding is still in its infancy compared with traditional crops. In this study, we evaluated the phenotypes of 12 oregano genotypes and generated F1 progenies by hybridization. The density of leaf glandular secretory trichomes and the essential oil yield in the 12 oregano genotypes varied from 97-1017 per cm2 and 0.17-1.67%, respectively. These genotypes were divided into four terpene chemotypes: carvacrol-, thymol-, germacrene D/β-caryophyllene-, and linalool/β-ocimene-type. Based on phenotypic data and considering terpene chemotypes as the main breeding goal, six oregano hybrid combinations were performed. Simple sequence repeat (SSR) markers were developed based on unpublished whole-genome sequencing data of Origanum vulgare, and 64 codominant SSR primers were screened on the parents of the six oregano combinations. These codominant primers were used to determine the authenticity of 40 F1 lines, and 37 true hybrids were identified. These 37 F1 lines were divided into six terpene chemotypes: sabinene-, β-ocimene-, γ-terpinene-, thymol-, carvacrol-, and p-cymene-type, four of which (sabinene-, β-ocimene-, γ-terpinene-, and p-cymene-type) were novel (i.e., different from the chemotypes of parents). The terpene contents of 18 of the 37 F1 lines were higher than those of their parents. The above results lay a strong foundation for the creating of new germplasm resources, constructing of genetic linkage map, and mapping quantitative trait loci (QTLs) of key horticultural traits, and provide insights into the mechanism of terpenoid biosynthesis in oregano.

Genotypic Variability Analysis of Lotus (Nelumbo nucifera Gaertn.) from Bangladesh using RAPD and SSR Markers

Lotus (Nelumbo nucifera Gaertn.) is a perennial aquatic plant with high ecological, medicinal, ornamental, and economic value from the prehistoric times. Different types of genotypes of lotus found in Bangladesh which represent a great variability. However, investigations on the variability of the lotus at genetic level are insufficient and limited in Bangladesh. In the current study, fourteen samples of lotus were collected from six different locations of Bangladesh were subjected to molecular analysis using codominant Simple Sequence Repeats (SSRs), as well as, dominant Random Amplified Polymorphic DNA (RAPD) markers to estimate the genetic diversity, and to test the genetic basis relationships among the germplasm. Analysis of SSRs showed a moderate level of polymorphism which was 68.12% and Nei’s genetic distance was ranging from 0.0328 to 0.7598 showing a significant level of variation among the genotypes. The germplasm collected from Kapasia identified as different and superior among the morphotypes. Moreover, RAPD analysis showed 60.44% polymorphism and Nei’s genetic distance was ranging from 0.0600 to 0.5743 indicating a moderate level of variability where yellow lotus was identified as distinct. Two Neighbor-Joining dendrograms were constructed using UPGMA method in which the germplasm were clustered into two main clades with 55% genetic similarity level for both RAPD and SSR markers. The current study was successful in establishing an efficient method for evaluating the variation and the genetic marker system to be used to identify core N. nucifera accessions. The method also could further assist in designing of suitable strategic programs to preserve the core lotus gene pool. Plant Tissue Cult. & Biotech. 32(1): 77-87, 2022 (June)

Molecular Characterization of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Collections from Nine Countries.

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat worldwide. To understand the worldwide distribution of its molecular groups, as well as the diversity, differentiation, and migration of the Pst populations, 567 isolates collected from nine countries (China, Pakistan, Italy, Egypt, Ethiopia, Canada, Mexico, Ecuador, and the U.S.) in 2010–2018 were genotyped using 14 codominant simple sequence repeat markers. A total of 433, including 333 new multi-locus genotypes (MLGs), were identified, which were clustered into ten molecular groups (MGs). The MGs and country-wise populations differed in genetic diversity, heterozygosity, and correlation coefficient between the marker and virulence data. Many isolates from different countries, especially the isolates from Mexico, Ecuador, and the U.S., were found to be identical or closely related MLGs, and some of the MGs were present in all countries, indicating Pst migrations among different countries. The analysis of molecular variance revealed 78% variation among isolates, 12% variation among countries, and 10% variation within countries. Only low levels of differentiation were found by the pairwise comparisons of country populations. Of the 10 MGs, 5 were found to be involved in sexual and/or somatic recombination. Identical and closely related MLGs identified from different countries indicated international migrations. The study provides information on the distributions of various Pst genetic groups in different countries and evidence for the global migrations, which should be useful in understanding the pathogen evolution and in stressing the need for continual monitoring of the disease and pathogen populations at the global scale.

High-Frequency Homologous Recombination Occurred Preferentially in Populus.

Homologous recombination (HR), the most significant event in meiosis, has important implications for genetic diversity and evolution in organisms. Heteroduplex DNA (hDNA), the product of HR, can be captured by artificially induced chromosome doubling during the development of the embryo sac to inhibit postmeiotic segregation, subsequently, and hDNAs are directly detected using codominant simple sequence repeat (SSR) markers. In the present study, two hybrid triploid populations derived from doubling the chromosomes of the embryo sac induced by high temperature in Populus tomentosa served as starting materials. Eighty-seven, 62, and 79 SSR markers on chromosomes 01, 04, and 19, respectively, that were heterozygous in the maternal parent and different from the paternal parent were screened to detect and characterize the hDNA in P. tomentosa. The results showed that the hDNA frequency patterns on chromosomes changed slightly when the number of SSR primers increased. The highest hDNA frequency occurred at the adjacent terminal on chromosomes, which was slightly higher than those at the terminals in the two genotypic individuals, and the hDNA frequency gradually decreased as the locus-centromere distance decreased. With the increase in the number of SSR markers employed for detection, the number of recombination events (REs) detected significantly increased. In regions with high methylation or long terminal repeat (LTR) retrotransposon enrichment, the frequency of hDNA was low, and high frequencies were observed in regions with low sequence complexity and high gene density. High-frequency recombination occurring at high gene density regions strongly affected the association between molecular markers and quantitative trait loci (QTLs), which was an important factor contributing to the difficulty encountered by MAS in achieving the expected breeding results.

Parasexual reproduction in Alternaria solani: Simple sequence repeat molecular evidence for haploidization

ABSTRACT Multiple alleles were constantly detected in Alternaria solani isolates by simple sequence repeat (SSR) analysis, and sectors were also observed in their subcultures. These preliminary results and observations point to a possible parasexual cycle in A. solani. In this study, codominant SSR markers were used as molecular markers on the chromosomes of A. solani and single-conidium subculture was used to simulate the mitosis process of A. solani in nature. The number of alleles at locus As-95236 changed from 2 to 1 as a molecular marker for haploidy of parasexuality of A. solani. Fifty monosporic F1 strains were tested. The results showed that two parent strains lost allele with a haploid probability of 38%. For F2 strains, the results showed that all four F1 strains lost allele with a haploid probability of 75%. Since sexual recombination of A. solani has not been found so far, the allele lost in the subcultures of A. solani isolates provides molecular evidence for the existence of parasexual reproduction in A. solani.

Genetic Dissection of Apomixis in Dandelions Identifies a Dominant Parthenogenesis Locus and Highlights the Complexity of Autonomous Endosperm Formation.

Apomixis in the common dandelion (Taraxacum officinale) consists of three developmental components: diplospory (apomeiosis), parthenogenesis, and autonomous endosperm development. The genetic basis of diplospory, which is inherited as a single dominant factor, has been previously elucidated. To uncover the genetic basis of the remaining components, a cross between a diploid sexual seed parent and a triploid apomictic pollen donor was made. The resulting 95 triploid progeny plants were genotyped with co-dominant simple-sequence repeat (SSR) markers and phenotyped for apomixis as a whole and for the individual apomixis components using Nomarski Differential Interference Contrast (DIC) microscopy of cleared ovules and seed flow cytometry. From this, a new SSR marker allele was discovered that was closely linked to parthenogenesis and unlinked to diplospory. The segregation of apomixis as a whole does not differ significantly from a three-locus model, with diplospory and parthenogenesis segregating as unlinked dominant loci. Autonomous endosperm is regularly present without parthenogenesis, suggesting that the parthenogenesis locus does not also control endosperm formation. However, the high recovery of autonomous endosperm is inconsistent with this phenotype segregating as the third dominant locus. These results highlight the genetic complexity underlying apomixis in the dandelion and underline the challenge of introducing autonomous apomixis into sexual crops.

Molecular Characterization of International Collections of the Wheat Stripe Rust Pathogen Puccinia striiformis f. sp. tritici Reveals High Diversity and Intercontinental Migration.

Puccinia striiformis f. sp. tritici causes stripe rust (yellow rust), one of the most important wheat diseases worldwide. To understand the genetic variation of the pathogen in a global scale, 283 P. striiformis f. sp. tritici isolates collected from 16 countries in eight geographic regions were genotyped using 24 codominant simple sequence repeat markers. The overall collection had a high level of genetic diversity, and the diversity levels in the Asian populations were generally higher than those of the other regions. Heterozygosity of isolates ranged from 0 to 75%, with an average of 46%. Mean heterozygosity in individual countries ranged from 34 to 59%. A total of 265 multilocus genotypes (MLGs) were detected, which were classified into eight molecular groups. Some of the molecular groups were present in all geographic regions. Moreover, many isolates from different regions were found to be identical or very closely related MLGs. Analysis of molecular variance revealed high variation within countries and intermediate variation between countries, but it revealed low and insignificant variation among geographic regions. Pairwise comparisons of regional populations detected considerable effective migrants and only low to moderate levels of differentiation. The molecular genotypes had a moderate level of correlation with the virulence phenotypes, and some of the molecular/virulence groups contained isolates from different continents. The results indicate tremendous migrations of P. striiformis f. sp. tritici and warrant the development of management strategies considering the global pathogen population.

Marker-Assisted Gene Pyramiding and the Reliability of Using SNP Markers Located in the Recombination Suppressed Regions of Sunflower (Helianthus annuus L.).

Rust caused by the fungus Puccinia helianthi and downy mildew (DM) caused by the obligate pathogen Plasmopara halstedii are two of the most globally important sunflower diseases. Resistance to rust and DM is controlled by race-specific single dominant genes. The present study aimed at pyramiding rust resistance genes combined with a DM resistance gene, using molecular markers. Four rust resistant lines, HA-R3 (carrying the R4 gene), HA-R2 (R5), HA-R8 (R15), and RHA 397 (R13b), were each crossed with a common line, RHA 464, carrying a rust gene R12 and a DM gene PlArg. An additional cross was made between HA-R8 and RHA 397. Co-dominant simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers linked to the target genes were used to discriminate between homozygotes and heterozygotes in F2 populations. Five pyramids with different combinations of rust resistance genes were selected in the homozygous condition through marker-assisted selection, and three of them were combined with a DM resistance gene PlArg: R4/R12/PlArg, R5/R12/PlArg, R13b/R12/PlArg, R15/R12, and R13b/R15. The pyramiding lines with the stacking of two rust and one DM genes were resistant to all known races of North American sunflower rust and all known races of the pathogen causing DM, potentially providing multiple and durable resistance to both rust and DM. A cluster of 12 SNP markers spanning a region of 34.5 Mb on chromosome 1, which co-segregate with PlArg, were tested in four populations. Use of those markers, located in a recombination suppressed region in marker selection, is discussed.

A novel aphid resistance locus in cowpea identified by combining SSR and SNP markers

AbstractThe utility of combining simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) marker genotyping was determined for genetically mapping a novel aphid (Aphis craccivora) resistance locus in cowpea breeding line SARC 1‐57‐2 and for introgressing the resistance into elite cultivars by marker‐assisted backcrossing (MABC). The locus was tagged with codominant SSR marker CP 171F/172R with a recombination fraction of 5.91% in an F2 population from ‘Apagbaala’ x SARC 1‐57‐2. A SNP‐genotyped biparental recombinant inbred line population was genotyped for CP 171F/172R, which was mapped to position 11.5 cM on linkage group (LG) 10 (physical position 30.514 Mb on chromosome Vu10). Using CP 171F/172R for foreground selection and a KASP‐SNP‐based marker panel for background selection in MABC, the resistance from SARC 1‐57‐2 was introduced into elite susceptible cultivar ‘Zaayura’. Five BC4F3 lines of improved ‘Zaayura’ that were isogenic except for the resistance locus region had phenotypes similar to SARC 1‐57‐2. This study identified a novel aphid resistance locus and demonstrated the effectiveness of integrating SSR and SNP markers for trait mapping and marker‐assisted breeding.

Local-Level Genetic Diversity and Structure of Matsutake Mushroom (Tricholoma matsutake) Populations in Nagano Prefecture, Japan, Revealed by 15 Microsatellite Markers

The annual yield of matsutake mushrooms (Tricholoma matsutake) has consistently decreased in Japan over the past few decades. We used 15 polymorphic and codominant simple sequence repeat (SSR) markers, developed using next-generation sequencing, to carry out genetic analyses of 10 populations in Nagano, Japan. Using the SSRs, we identified 223 genotypes, none of which was observed in more than one population. The mean expected heterozygosity and standardized allelic richness values were 0.67 and 4.05, respectively. Many alleles appeared in only one of the 10 populations; 34 of these private alleles were detected with a mean number per population of 3.4. The fixation index (FST) and standardized genetic differentiation (G′ST) values were 0.019 and 0.028, respectively. Analysis of molecular variance (AMOVA) showed that the contribution of among population, among genets within a population, and within genets variation to the total variation was 2.91%, 11.62%, and 85.47%, respectively, with genetic differentiation being detected for all sources. Twenty-eight of 45 pairwise FST values were significantly larger than zero, and no pattern of isolation by distance was detected among the 10 populations. Bayesian-based clustering did not show clear differences among populations. These results suggest that reestablishment of a colony would be best accomplished by transplantation within a field; if this is not possible, then transplantation from within several dozen kilometers will cause little damage to the original population genetic structure.

Evidence and consequences of self-fertilisation in the predominantly outbreeding forage legume Onobrychis viciifolia.

BackgroundSainfoin (Onobrychis viciifolia) is a promising alternative forage plant of good quality, moderate nutrient demand and a high content of polyphenolic compounds. Its poor adoption is caused by the limited availability of well performing varieties. Sainfoin is characterised as tetraploid and mainly outcrossing, but the extent of self-fertilisation and its consequences was not investigated so far. This study aimed at assessing the rate of self-fertilisation in sainfoin under different pollination regimes and at analysing the consequences on plant performance in order to assist future breeding efforts.MethodsThe self-fertilisation rate was assessed in three sainfoin populations with artificially directed pollination (ADP) and in three populations with non-directed pollination (NDP). Dominant SRAP (sequence-related amplified polymorphism) and codominant SSR (simple sequence repeats) markers were used to detect self-fertilisation in sainfoin for the first time based on molecular marker data.ResultsHigh rates of self-fertilisation of up to 64.8 % were observed for ADP populations in contrast to only up to 3.9 % for NDP populations. Self-fertilisation in ADP populations led to a reduction in plant height, plant vigour and, most severely, for seed yield.ConclusionsAlthough sainfoin is predominantly outcrossing, self-fertilisation can occur to a high degree under conditions of limited pollen availability. These results will influence future breeding efforts because precautions have to be taken when crossing breeding material. The resulting inbreeding depression can lead to reduced performance in self-fertilised offspring. Nevertheless the possibility of self-fertilisation also offers new ways for hybrid breeding based on the development of homogenous inbred lines.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-015-0275-z) contains supplementary material, which is available to authorized users.

A QTL with major effect on reducing leaf rust severity on the short arm of chromosome 1A of wheat detected across different genetic backgrounds and diverse environments.

Selection for QLr.cau - 1AS (a major QTL detected in wheat for reducing leaf rust severity) based on the DNA marker gpw2246 was as effective as selection for Lr34 based on cssfr5. Leaf rust is an important disease of wheat worldwide. Utilization of slow-rusting resistance constitutes a strategy to sustainably control this disease. The American wheat cultivar Luke exhibits slow leaf-rusting resistance at the adult plant stage. The objectives of this study were to detect and validate QTL for the resistance in Luke. Three winter wheat populations were used, namely, 149 recombinant inbred lines (RILs) derived from the cross Luke × Aquileja, 307 RILs from Luke × AQ24788-83, and 80 F2:3 families selected from Lingxing66 × KA298. Aquileja and Lingxing66 are highly susceptible to leaf rust. AQ24788-83 shows high (susceptible) infection type but contains the slow-rusting gene Lr34 as diagnosed by the gene-specific marker cssfr5. KA298, an F9 RIL selected from Luke × AQ24788-83, contains Lr34 and QLr.cau-1AS (a major QTL originated from Luke, this study). These wheats were evaluated for leaf rust in 12 field and greenhouse environments involving four locations and five seasons. Genotyping was done using simple sequence repeat (SSR) and diversity arrays technology markers. Of the detected QTLs, QLr.cau-1AS was significant consistently across all the genetic backgrounds, test environments, and likely a wide range of pathogen races. QLr.cau-1AS explained 22.3-55.2% of leaf rust phenotypic variation, being comparable to Lr34 in effect size. A co-dominant SSR marker (gpw2246, http://wheat.pw.usda.gov/GG2/index.shtml ) was identified to be tightly linked to QLr.cau-1AS. Selection based on gpw2246 for QLr.cau-1AS was as effective as the selection based on cssfr5 for Lr34. QLr.cau-1AS will be helpful for increasing the genetic diversity of slow leaf-rusting resistance in wheat breeding programs.

Molecular mapping of a recessive stripe rust resistance gene yrMY37 in Chinese wheat cultivar Mianmai 37

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most destructive diseases of wheat (Triticum aestivum L.) in many cool and temperate regions of the world. Resistant cultivars are the most effective, economical and environmentally friendly means of controlling the disease. Chinese wheat cultivar Mianmai 37 is resistant at all growth stages to all prevalent Chinese Pst races including v26, a new Pst race virulent to resistance genes Yr24/Yr26. Genetic analysis of the F1, F2 and F2:3 populations from a cross between Mianmai 37 and susceptible line Mingxian 169 indicated that resistance to Pst race v26 was conferred by a single recessive gene, temporarily designated yrMY37. Simple sequence repeat (SSR) marker analysis placed yrMY37 on chromosome 7BL near the centromere. Eight co-dominant genomic SSR markers, Xgwm400, Xwmc758, Xwmc476, Xgwm297, Xbarc267, Xwmc364, Xwmc696 and Xwmc396, were linked with yrMY37. The closest SSR loci Xbarc267 and Xgwm297 flanked the resistance gene at 0.38 and 0.78 cM, respectively. A seedling test with 22 Pst races indicated that the reaction patterns of Mianmai 37 were different from those of lines carrying resistance genes Yr2, Yr6, Yr67 and YrZH84 on chromosome 7B. As there is no recessive stripe rust resistance gene reported on 7BL so far, we believe that yrMY37 is most likely a new stripe rust resistance gene.

Registration of BARBREN-713 Germplasm Line of Upland Cotton Resistant to Reniform and Root-Knot Nematodes

Cotton (Gossypium hirsutum L.) germplasm line BARBREN-713 (Reg. No. GP-987, PI 671965) was developed and released by the USDA–ARS, Mississippi Agricultural and Forestry Experiment Station, Texas A&M AgriLife Research, and Cotton Incorporated in 2012. The objective of the release was to provide public and private breeders with an agronomically desirable germplasm that is resistant to both the reniform nematode (Rotylenchulus reniformis Linford and Oliveira) and the root-knot nematode [Meloidogyne incognita (Kofoid and White) Chitwood]. The line also has excellent seedling vigor in fields infested with nematodes and fungal root rot pathogens, such as Thielaviopsis basicola, Rhizoctonia solani and Fusarium spp. Resistance to reniform nematode was transferred from G. barbadense GB713 (PI 608139) and is associated primarily with the Ren2GB713 gene on chromosome 21. Resistance to root-knot nematode was transferred from the germplasm line M-315 RNR (PI 592514), ‘LA 887’, or ‘Acala Nem-X’ and is associated primarily with the Mi-1 gene on chromosome 11. The codominant simple sequence repeat markers, BNL 3279_105 and CIR 316_202, respectively, were closely linked to the resistance genes. A single nucleotide polymorphism marker, Gl-187401, also was developed to detect the Ren2GB713 gene. In controlled environment assays, BARBREN-713 suppressed reproduction of both nematodes by 90% or more. It also reduced reniform nematode populations in the field at eight locations in four states. The line has fiber quality similar to M-315 RNR but yielded more than M-315 RNR in reniform nematode-infested fields.

Marker assisted gene pyramiding for enhanced Tomato leaf curl virus disease resistance in tomato cultivars

The present research is aimed towards molecular marker assisted pyramiding Tomato leaf curl virus (ToLCV) disease resistance genes into two ToLCV susceptible tomato (Solanum lycopersicum L.) cvs. Pbc and H-86 (resistance genes recipient parents). Resistance gene donors were EC-538408 (Solanum chilense) and EC-520061 (S. peruvianum) in the case of cv. Pbc, and EC-520061 (S. peruvianum) and H-24 (S. lycopersicum) in the case of cv. H-86. A ToLCV resistance gene associated co-dominant simple sequence repeat (SSR) marker SSR-218 was used to discriminate between homozygotes and heterozygotes at the seedling stage prior to pollination, which enabled the rejection of nontarget back crosses and pyramiding progenies of the crosses PbcxEC-520061 and H-86xEC-520061, whereas SSR-306 was used for the cross PbcxEC-538408. Ty-2 gene cleaved amplified polymorphic sequences (CAPS) marker was used for the cross H-86xH-24. Out of 279 pyramiding progenies of the cross PbcxEC-538408/PbcxEC-520061, total 91 plants showed the presence of both resistance allele 1 and 2 along with both susceptibility alleles, and in 243 pyramiding progenies of the cross H-86xEC-520061/H-86xH-24, total 82 plants showed the presence of both resistance allele 1 and Ty-2 along with both susceptible alleles. The pyramiding lines that carried both pyramided resistance genes were resistant to tomato leaf curl disease throughout its life cycle.

Registration of LONREN-1 and LONREN-2 Germplasm Lines of Upland Cotton Resistant to Reniform Nematode

Cotton (Gossypium hirsutum L.) germplasm lines LONREN-1 (Reg. No. GP-977, PI 669509) and LONREN-2 (Reg. No. GP-978, PI 669510) were developed and released by the USDA–ARS, Texas Agricultural Experiment Station and Cotton Incorporated in 2007 to provide breeders with desirable germplasm resistant to the reniform nematode (Rotylenchulus reniformis Linford and Oliveira). The resistance was transferred from wild G. longicalyx via a triple-species hybrid. Crosses, backcrosses, and single plant selections were used to develop the F2 progeny used for seed production. Resistance was followed with the codominant simple sequence repeat BNL 3279_114 marker, located 1.4 cM proximal and the phenotypic marker ‘greenfuzz’ (LTCOL_F) located 4.5 cM distal to the Renlon resistance gene on chromosome 11. A single nucleotide polymorphism marker also was developed for rapid screening of large numbers of seed. The introgressed chromosome segment is smaller in LONREN-2 than in LONREN-1. Both lines reduced reniform populations by 95% in growth chamber bioassays and by 50 to 90% in fields. In the absence of nematodes in the field, growth rate, yield, and fiber quality of the lines were similar to that of the ‘Fibermax 958’ parent. In the presence of reniform nematodes in the field, the lines often showed stunting and yield losses, probably due to enhanced severity of fungal seedling diseases, especially Thielaviopsis root rot. The seedling diseases in LONRENs were diminished by control measures such as fungicides, nematicides, and crop rotation with corn or sorghum, and were negligible in a second year of planting in the same field.

High-resolution mapping of the dull fruit skin gene D in cucumber (Cucumis sativus L.)

Dull/glossy fruit skin is a highly valuable external quality trait that affects the market value of cucumbers. In this study, genetic analysis showed that one single dominant gene, D (dull fruit skin), determines the dull fruit skin trait in cucumber. By combining bulked segregant analysis with 11 published polymorphic molecular markers on chromosome 5, the D/d gene was preliminarily mapped between markers SCZ69 and SSR16203, at genetic distances of 0.3 and 0.6 cM, respectively. Subsequently, a larger F2 (S06 × S94) population (842 individuals in total) was used for high-resolution mapping of the D/d gene. Finally, the D/d gene was fine-mapped between markers SSR37 and SSR112, at a physical distance of 244.9 kb (containing 31 candidate genes), using eight newly developed polymorphic simple sequence repeat (SSR) markers between SCZ69 and SSR16203. Based on semi-quantitative RT-PCR analysis, the possible candidate gene D was identified as Csa016880 or Csa016887. Meanwhile, validity analysis of the markers SSR37 and SSR112 was performed with 72 dull/glossy fruit lines, and showed that the two co-dominant SSR markers could be used for marker-assisted selection of the dull/glossy fruit trait in cucumber breeding. Moreover, this study will be helpful for cloning of the D gene in cucumber.

Pinus monticola pathogenesis-related gene PmPR10-2 alleles as defense candidates for stem quantitative disease resistance against white pine blister rust (Cronartium ribicola)

White pine blister rust, caused by the invasive fungus Cronartium ribicola, has been responsible for extremely high mortality of native western white pine (Pinus monticola) and other five-needle pines in natural stands throughout western North America. The presence of this non-native fungus has also led to greatly restricted use of western white pine for reforestation. A few families of defense proteins have been found as functional candidates involved in tree resistance to rust infection. Here we report genetic variation of a gene encoding a family 10 pathogenesis-related (PR) protein (PmPR10-2) in open-pollinated seed families with different levels of stem quantitative disease resistance (QDR). Six novel alleles and five common genotypes were identified inside the PmPR10-2 locus: these genetic variations included 33 single nucleotide polymorphisms (SNPs) throughout the gene regions and copy variation of a rare octanucleotide simple sequence repeat (SSR), 5′-AATTATTT-3′, in the gene intron. PmPR10-2 exhibited a moderate level (average r 2 = 0.42) of linkage disequilibrium. Two-thirds of the identified SNPs and the SSR marker were significantly associated with stem QDR levels. The PmPR10-2 genotype (H3:H3) exhibited the highest level of stem QDR (P < 0.01). Cost-effective and co-dominant SSR markers were developed and used for genotyping the PmPR10-2 locus using simple PCR, providing a potential molecular tool for accelerating screening efforts of white pine resistance against C. ribicola.

Development of selective markers linked to a major QTL for parthenocarpy in eggplant (Solanum melongena L.)

Parthenocarpy, the ability to set fruits without pollination, is a useful trait for setting fruit under unfavorable conditions. To identify the loci controlling parthenocarpy in eggplant (Solanum melongena L.), we constructed linkage maps by using co-dominant simple sequence repeat and single nucleotide polymorphism markers in F(2) populations derived from intraspecific crosses between two non-parthenocarpic lines (LS1934 and Nakate-Shinkuro) and a parthenocarpic line (AE-P03). Total map distances were 1,414.6 cM (ALF2: LS1934 x AE-P03) and 1,153.8 cM (NAF2: Nakate-Shinkuro x AE-P03), respectively. Quantitative trait locus (QTL) analyses revealed two QTLs on chromosomes 3 and 8, which we denoted as Controlling parthenocarpy3.1 (Cop3.1) and Cop8.1, respectively. The percentage of phenotypic variance explained (PVE) of Cop3.1 was 6.3% in ALF2 (LOD = 4.2) and 10.6% in NAF2 (LOD = 3.0). The PVE of Cop8.1 was 45.7% in ALF2 (LOD = 23.8) and 29.7% in NAF2 (LOD = 7.9). Using a population of backcross inbred lines, we confirmed the effect of Cop8.1, but there was no evidence to support the contribution of Cop3.1. We need to verify the effect of Cop3.1 under various temperature conditions. In addition, we clarified the effectiveness of selective SSR markers, emf21H22 and emh11J10, mapped on each side of Cop8.1 in other F(2) populations derived from various parental combinations. This is the first report concerning QTL analysis of parthenocarpy in eggplant using molecular markers. It will be useful in marker-assisted selection and in revealing the genomic mechanism underlying parthenocarpy in eggplant.