Maker-assisted Selection Research Articles

RNA-Seq Analysis Identifies Differentially Expressed Genes in the Longissimus dorsi of Wagyu and Chinese Red Steppe Cattle.

Meat quality has a close relationship with fat and connective tissue; therefore, screening and identifying functional genes related to lipid metabolism is essential for the production of high-grade beef. The transcriptomes of the Longissimus dorsi muscle in Wagyu and Chinese Red Steppe cattle, breeds with significant differences in meat quality and intramuscular fat deposition, were analyzed using RNA-seq to screen for candidate genes associated with beef quality traits. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the 388 differentially expressed genes (DEGs) were involved in biological processes such as short-chain fatty acid metabolism, regulation of fatty acid transport and the peroxisome proliferator-activated receptor (PPAR) signaling pathway. In addition, crystallin alpha B (CRYAB), ankyrin repeat domain 2 (ANKRD2), aldehyde dehydrogenase 9 family member A1 (ALDH9A1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) were investigated for their effects on intracellular triglyceride and fatty acid content and their regulatory effects on genes in lipogenesis and fatty acid metabolism pathways. This study generated a dataset from transcriptome profiling of two cattle breeds, with differing capacities for fat-deposition in the muscle, and revealed molecular evidence that CRYAB, ANKRD2, ALDH9A1 and EHHADH are related to fat metabolism in bovine fetal fibroblasts (BFFs). The results provide potential functional genes for maker-assisted selection and molecular breeding to improve meat quality traits in beef cattle.

Quantitative Trait Locus Mapping for Drought Tolerance in Soybean Recombinant Inbred Line Population.

Improving drought stress tolerance of soybean could be an effective way to minimize the yield reduction in the drought prevailing regions. Identification of drought tolerance-related quantitative trait loci (QTLs) is useful to facilitate the development of stress-tolerant varieties. This study aimed to identify the QTLs for drought tolerance in soybean using a recombinant inbred line (RIL) population developed from the cross between a drought-tolerant ‘PI416937’ and a susceptible ‘Cheonsang’ cultivar. Phenotyping was done with a weighted drought coefficient derived from the vegetative and reproductive traits. The genetic map was constructed using 2648 polymorphic SNP markers that distributed on 20 chromosomes with a mean genetic distance of 1.36 cM between markers. A total of 10 QTLs with 3.52–4.7 logarithm of odds value accounting for up to 12.9% phenotypic variance were identified on seven chromosomes. Five chromosomes—2, 7, 10, 14, and 20—contained one QTL each, and chromosomes 1 and 19 harbored two and three QTLs, respectively. The chromosomal locations of seven QTLs overlapped or located close to the related QTLs and/or potential candidate genes reported earlier. The QTLs and closely linked markers could be utilized in maker-assisted selection to accelerate the breeding for drought tolerance in soybean.

Construction of a genetic linkage map and QTL mapping for sex indicate the putative genetic pattern of the F1 hybrid Scylla (Scylla serrata ♀ × S. paramamosain ♂)

To provide a valuable framework for genome sequence assembly towards the elucidation of the F1 hybrid Scylla (Scylla serrata ♀ × S. paramamosain ♂) genome as well as a reference for QTL mapping and maker-assisted selection, herein F1 hybrid offspring were obtained and used to construct the first genetic linkage map of hybrid Scylla. We presented a sex-averaged genetic linkage map with 49 linkage groups (LGs) covering 5574 SNP markers. The male map consisted of 40 LGs, whereas the female map comprises 22 LGs. The high quality of this genetic linkage map was verified by the low proportion of distorted markers, the strong linkage relationship between adjacent markers on each LG, and the consistent source of the larger segment in each individual. All sex-linked markers distributed in three QTL regions were located on LG12, indicating the chromosome corresponding to LG12 seems to be the sex chromosome of the F1 hybrid offspring. A sex-linked LG comparison of the genetic maps between F1 hybrid offspring and the S. paramamosain suggested the conformation of a ZW/ZZ sex determination system in F1 hybrid offspring. Based on the high quality of this genetic linkage map, we described the putative genetic pattern of F1 hybrid diploid offspring. The putative genetic pattern argues the proposition that a formation of chromosome synapsis among different species might be an initial inducement for the divergence of chromosomal forms.

Genetic Mapping and Discovery of the Candidate Gene for Black Seed Coat Color in Watermelon (Citrullus lanatus)

Seed coat color is an important trait highly affecting the seed quality and flesh appearance of watermelon (Citrullus lanatus). However, the molecular regulation mechanism of seed coat color in watermelon is still unclear. In the present study, genetic analysis was performed by evaluating F1, F2 and BC1 populations derived from two parental lines (9904 with light yellow seeds and Handel with black seeds), suggesting that a single dominant gene controls the black seed coat. The initial mapping result revealed a region of interest spanning 370 kb on chromosome 3. Genetic mapping with CAPS and SNP markers narrowed down the candidate region to 70.2 kb. Sequence alignment of the three putative genes in the candidate region suggested that there was a single-nucleotide insertion in the coding region of Cla019481 in 9904, resulting in a frameshift mutation and premature stop codon. The results indicated that Cla019481 named ClCS1 was the candidate gene for black seed coat color in watermelon. In addition, gene annotation revealed that Cla019481 encoded a polyphenol oxidase (PPO), which involved in the oxidation step of the melanin biosynthesis. This research finding will facilitate maker-assisted selection in watermelon and provide evidence for the study of black seed coat coloration in plants.

Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat.

Simple SummaryAs a major gene to regulate the muscle mass of animals, Myostatin (MSTN) plays a negative role in regulating the number and size of skeletal myocytes. Additionally, it is reported that mutations of MSTN gene contribute to the double-muscling (DBM) phenomenon. Therefore, mutations of MSTN gene will always be one of the hot spots. A 5 bp indel (c. –120 ins) in the 5’ untranslated region (5’ UTR) of goat MSTN gene was reported to relate to the growth traits of goat. However, all the sample sizes were limited. Herein, this study firstly enlarged the sample size (n = 1074, Shaanbei White Cashmere goat) to uncover the indel location, as well as its association with growing performance. Based on the data, the 5 bp insertion mutation in goat MSTN gene was significantly associated with the body height, height at hip cross, and chest width index in SBWC (p < 0.05), hinted that this insertion could be assigned to an effective molecular marker for growth trait in goat rearing.Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5’ untranslated region (5’ UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats.

Chromosomal Locations and Interactions of Four Loci Associated With Seed Coat Color in Watermelon.

Different species of edible seed watermelons (Citrullus spp.) are cultivated in Asia and Africa for their colorful nutritious seeds. Consumer preference varies for watermelon seed coat color. Therefore, it is an important consideration for watermelon breeders. In 1940s, a genetic model of four genes, R, T, W and D, was proposed to elucidate the inheritance of seed coat color in watermelon. In this study, we developed three segregating F2 populations: Sugar Baby (dotted black seed, RRTTWW) × plant introduction (PI) 482379 (green seed, rrTTWW), Charleston Gray (dotted black seed, RRTTWW) × PI 189225 (red seed, rrttWW), and Charleston Gray (dotted black seed, RRTTWWdd) × UGA147 (clump seed, RRTTwwDD) to re-examine the four-gene model and to map the four genes. In the dotted black × green population, the dotted black seed coat color (R_) is dominant to green seed coat color (rr). In the dotted black × red population, the dominant dotted black seed coat color and the recessive red seed coat color segregate for the R and T genes, where the R gene is dominantly epistatic to the T gene. However, the inheritance of the T locus did not fit the four-gene model, thus we named it T1. In the dotted black × clump population, the clump seed coat color and the dotted black seed coat color segregate for W and D, where D is recessively epistatic to W. The R, T1, W, and D loci were mapped on chromosomes 3, 5, 6, and 8, respectively, using QTL-seq and genotyping-by-sequencing (GBS). Kompetitive Allele Specific PCR (KASP™) assays and SNP markers linked to the four loci were developed to facilitate maker-assisted selection (MAS) for watermelon seed coat color.

High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq

BackgroundAlfalfa (Medicago sativa L.) is an important forage crop grown worldwide. Alfalfa is called the “queen of forage crops” due to its high forage yield and nutritional characteristics. The aim of this study was to undertake quantitative trait loci (QTL) mapping of yield and yield-related traits in an F1 population of two alfalfa varieties that differ in their yield and yield-related traits.ResultsWe constructed a high-density linkage map using single nucleotide polymorphism (SNP) markers generated by restriction-site associated DNA sequencing (RAD-seq). The linkage map contains 4346 SNP and 119 simple sequence repeat (SSR) markers, with 32 linkage groups for each parent. The average marker distances were 3.00 and 1.32 cM, with coverages of 3455 cM and 4381 cM for paternal and maternal linkage maps, respectively. Using these maps and phenotypic data, we identified a total of 21 QTL for yield and yield components, including five for yield, five for plant height, five for branch number, and six for shoot diameter. Among them, six QTL were co-located for more than one trait. Five QTL explained more than 10% of the phenotypic variation.ConclusionsWe used RAD-seq to construct a linkage map for alfalfa that greatly enhanced marker density compared to previous studies. This high-density linkage map of alfalfa is a useful reference for mapping yield-related traits. Identified yield-related loci could be used to validate their usefulness in developing markers for maker-assisted selection in breeding populations to improve yield potential in alfalfa.

Development and utilization of functional KASP markers to improve rice eating and cooking quality through MAS breeding

There is a steady demand for high-quality rice varieties though consumers’ preference for high-quality rice varies from regions. The improvement of the quality of rice, especially its eating and cooking quality (ECQ), is an important breeding target as rice is mainly consumed in cooked form. The development and utilization of breeder-friendly and high-throughput marker systems play a pivotal role in marker-assisted breeding of rice cultivars, with pyramids of valuable genes affecting rice ECQ. In this study, we developed functional markers based on the Kompetitive Allele-Specific PCR (KASP) method for three principal genes, Wx, BADH2 and ALK, affecting ECQ in rice. The accuracy of all KASP markers was verified and confirmed with Sanger sequencing. A diverse rice panel consisting of 38 indica cultivars, 9 japonica cultivars and 1 Javanica cultivar were used to assess the validity of these markers for genotyping. The results showed that the functional KASP markers of Wx, ALK and BADH2 could effectively distinguish the different alleles. The genotyping results highly coincided with the phenotypic traits of rice eating and cooking quality. Eight rice entries harboring 3 favorable alleles were identified and superior rice restorers with improved ECQ were bred via functional marker genotyping. Breeders can develop rice cultivars that have desirable ECQ, customized to meet the market requirements in target regions. Hence, the development of these 3 applicable KASP functional markers based on allelic variation would be valuable for improving rice eating and cooking quality through maker-assisted selection to carter various consumer preferences especially in Asian areas.

Resistance of the wild tomato Solanum habrochaites to Phytophthora infestans is governed by a major gene and polygenes.

This work aimed to study the inheritance of resistance to Phytophthora infestans in tomato plants, using the maximum likelihood estimation function. The susceptible cultivar Santa Clara (Solanum lycopersicum) was used as the female genitor and the P. infestans resistant S. habrochaites f. glabratum accession (BGH 6902) as the male genitor. F1 plants from the crossing were self-pollinated to produce F2 progenies, and also backcrossed with PR and PS to produce BC1:R and BC1:S generations, respectively. The tomato plants were inoculated 50 days after transplanting. Disease severity was evaluated via a diagrammatic scale. Comparison of the genetic models created using the maximum likelihood function revealed that the inheritance of resistance to P. infestans in S. habrochaites is conferred by a major gene with additive and dominance effects, polygenes with additive effects, plus the environmental effect. Vertical resistance can be explored using genes with major effects. Programs of recurrent and maker-assisted selection are considered efficient strategies with which to select genotypes that hold P. infestans resistance conferred by polygenes.

Dominance and Epistasis Interactions Revealed as Important Variants for Leaf Traits of Maize NAM Population.

Leaf orientation traits of maize (Zea mays) are complex traits controlling by multiple loci with additive, dominance, epistasis, and environmental interaction effects. In this study, an attempt was made for identifying the causal loci, and estimating the additive, non-additive, environmental specific genetic effects underpinning leaf traits (leaf length, leaf width, and upper leaf angle) of maize NAM population. Leaf traits were analyzed by using full genetic model and additive model of multiple loci. Analysis with full genetic model identified 38∼47 highly significant loci (-log10PEW > 5), while estimated total heritability were 64.32∼79.06% with large contributions due to dominance and dominance related epistasis effects (16.00∼56.91%). Analysis with additive model obtained smaller total heritability ( ≙ 18.68∼29.56%) and detected fewer loci (30∼36) as compared to the full genetic model. There were 12 pleiotropic loci identified for the three leaf traits: eight loci for leaf length and leaf width, and four loci for leaf length and leaf angle. Optimal genotype combinations of superior line (SL) and superior hybrid (SH) were predicted for each of the traits under four different environments based on estimated genotypic effects to facilitate maker-assisted selection for the leaf traits.

Evaluation of novel SNPs and haplotypes within the &amp;lt;i&amp;gt;ATBF1&amp;lt;/i&amp;gt; gene and their effects on economically important production traits in cattle

Abstract. AT motif binding factor 1 (ATBF1) gene can promote the expression level of the growth hormone 1 (GH1) gene by binding to the enhancers of the POU1F1 and PROP1 genes; thus, it affects the growth and development of livestock. Considering that the ATBF1 gene also has a close relationship with the Janus kinase–signal transductor and activator of transcription (JAK–STAT) pathway, the objective of this work was to identify novel single-nucleotide polymorphism (SNP) variations and their association with growth traits in native Chinese cattle breeds. Five novel SNPs within the ATBF1 gene were found in 644 Qinchuan and Jinnan cattle for first time using 25 pairs of screening and genotyping primers. The five novel SNPs were named as AC_000175:g.140344C&gt;G (SNP1), g.146573T&gt;C (SNP2), g.205468C&gt;T (SNP3), g.205575A&gt;G (SNP4) and g.297690C&lt;T (SNP5). Among them, SNP1 and SNP2 were synonymous coding SNPs, while SNP5 was a missense coding SNP, and the other SNPs were intronic. Haplotype analysis found 18 haplotypes in the two breeds, and three and five closely linked loci were revealed in Qinchuan and Jinnan breeds, respectively. Association analysis revealed that SNP1 was significantly associated with the height across the hip in Qinchuan cattle. SNP2 was found to be significantly related to chest circumference and body side length traits in Jinnan cattle. SNP3 was found to have significant associations with four growth traits in Qinchuan cattle. Moreover, the different combined genotypes, SNP1–SNP3, SNP1–SNP4 and SNP2–SNP5 were significantly associated with the growth traits in cattle. These findings indicated that the bovine ATBF1 gene had marked effects on growth traits, and the growth-trait-related loci can be used as DNA markers for maker-assisted selection (MAS) breeding programs in cattle.

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.

Screening and identification of microsatellite markers associated with cold tolerance in Nile tilapia Oreochromis niloticus.

Tilapia is an important fish cultured in tropical and subtropical areas. Cold sensitivity limits the expansion of tilapia culture into colder regions of the world, and mass mortalities of cultured tilapia have been reported due to severe cold currents in winter. Since the late 1990s, several strains of Nile tilapia have been domesticated to improve the ability to adapt to low temperatures. Previous studies revealed that these varieties were more cold-tolerant than the founder population and overwintered naturally well in ponds in the west-south area of Guangdong Province. In this study, to develop tilapia strains with improved cold tolerance for breeding programs through marker-assisted selection, two microsatellite markers, UNH916 and UNH999, showed complete co-segregation with cold tolerance among the polymorphic microsatellite primers. Our results provide a foundation for identifying resistant gene(s) linked with these markers, as well as identifying simple sequence repeat markers associated with cold tolerance that can be used for maker-assisted selection programs in tilapia breeding to increase the growing range and productivity of tilapia aquaculture.

Next-generation Sequencing for Molecular Marker Development in Maize Inbred H99

Next Generation Sequencing(NGS) has provided an effective approach to reveal the large scale of DNA polymorphic loci used as molecular markers to distinguish the genetic variations among different genotypes. Maize inbred line H99 is a common transgenic genotype with its desirable regeneration capacity. However, the genome sequence of H99 is unsequenced, which lags the molecular marker development for further maker assisted selection. Here, we used next generation sequencing to resequence H99 whole genome. The contigs assembled with SOAPdenovo2 were further scanned for potential SSR loci by MISA software. Out of 8268 SSR loci, 4043 site-specific primers flanking SSR loci were designed and surveyed in silico for locus polymorphism among H99, B73, and Mo17. Around 2699 SSR loci showed the polymorphism among above three genotypes. Twenty primer pairs from 20 arms of maize chromosomes were selected and validated, and 19 primers amplified the predicted fragments. In addition, we physically mapped and annotated the polymorphic SSR loci, and elucidated the loci distribution in genome. Taken all together, the new developed SSR primers and their information, as a complement to previous ones, were expected to be beneficial to map based cloning and marker-assisted selection.

Marker assisted characterization of chickpea genotypes for wilt resistance

Marker assisted characterization of six chickpea genotypes differing for Fusarium wilt reaction was carried out using seven molecular markers reported by earlier workers linked to disease resistant/susceptibility. In the present study, four different markers (namely, CS-27, UBC-170, CS-27A and UBC-825) linked to susceptibility and three microsatellite based markers (TA-59, TA-96 and TR-19) linked to resistance allele were validated. It was observed that two Random Amplified Polymorphic DNA (RAPD) markers, CS-27 and UBC-170 and one sequenced characterized amplified region (SCAR) CS-27A 700 gave amplification of 700, 550 and 700 bp, respectively in susceptible genotype only as reported by earlier worker. The inter simple sequence repeat (ISSR) marker UBC-825 produced amplification of 1200 bp in susceptible genotypes (JG-62 and GG 4) and intermediate genotype (Chaffa). Three sequence tagged microsatellites site (STMS) primers (TA-59, TA-96 and TR-19) gave specific allele in wilt resistant genotypes. The PCR amplification of TA-59 primer generated two alleles, out of which the allele of 258 bp was present only in resistance genotypes. The alleles of 265 bp amplified by primer TA-96 was present only in resistance genotypes and absent in other genotypes. The marker TR-19 amplified allele of 227 bp in resistant genotypes. Further, the sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE) analysis of seed storage protein showed a difference in protein profile among studied genotypes but none of polypeptide fragment was specific to wilt resistance or susceptibility. In present study, the reported markers linked to susceptibility and resistance proved their effectiveness and further can be exploited for maker assisted selection (MAS) of wilt resistance breeding in chickpea. Keywords: Chickpea, Fusarium wilt, molecular markers, resistance, sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS PAGE). Afr. J. Biotechnol. Vol. 12 No. 50

QTL analysis for gossypol and protein contents in upland cottonseeds with two different genetic systems across environments

Genetically improved cottonseed with high protein content and low or no gossypol content could be suitably processed for human and animal consumption. In the present study, quantitative trait loci (QTL) associated with the genetic effects including QTL main effects and QTL × environment interaction effects from tetroploid maternal plant genome and tetroploid embryo genome were simultaneously identified for protein and gossypol contents of cottonseeds. This is to help understand the QTL and QTL × environment interactions from embryo and maternal genomes for these two traits, and provide more effective information for their improvement in cottonseed through maker-assisted selection. The experiment was carried out on an immortal F2 population comprising 376 lines obtained among 188 recombinant inbred lines (RILs) derived from a cross between parents HS46 and MARKCBUCAG8US-1-88, grown in 2009 and 2010. Twelve QTL for protein content (PC) and ten for gossypol content (GC) were detected using a genetic linkage map comprising 388 molecular markers. Among them, five QTL for gossypol content and six QTL for protein content were found in two different environments, explaining 62.95 and 58.52 % of phenotypic variances, respectively. A total of nine QTL were associated with these two traits, which were subsequently mapped to chromosome 3, 5, 6, 15, 18, 22 and 25. Six of these QTL were also found to have environmental interaction effects. The results from this study could be very useful in adopting effect strategies for protein improvement and gossypol elimination in cottonseeds.

Inheritance and fine mapping of a restorer-of-fertility (Rf) gene for the cytoplasmic male sterility in soybean

The cytoplasmic male sterility (CMS) line FuCMS5A and its restorer line FuHui9 were crossed to produce a segregating F2 population for pollen fertility assay and the genetic mapping of restorer-of-fertility (Rf) gene. Results showed that the individual F2 plants were fertile or semi-fertile based on their pollen fertility characteristics. The average ratios of viable pollen were 96.90% and 50.00% for each class of individuals. The segregation of F2 plants showed a good fit to a 1:1 ratio, which reflects a typical heredity pattern of gametophytic CMS with fertility restorer being controlled by a single dominant gene. Using bulk segregation analysis (BSA) and genetic mapping, the Rf gene was mapped on molecular linkage group J (chromosome 16), between the simple sequence repeat (SSR) makers BARCSOYSSR-16-1064 and BARCSOYSSR-16-1082 with the distances of 0.59 and 0.83cM, respectively. Four SSR markers (BARCSOYSSR-16-1070, Sctt011, BARCSOYSSR-16-1076 and BARCSOYSSR-16-1077) were cosegregating with this Rf gene in the mapping population. These makers will greatly facilitate the maker assisted selection procedures in CMS breeding programs and it lays a foundation for further map-base cloning of the Rf gene.

Genetic map of lps3: a new short petiole gene in soybeans

The short petiole trait is valuable for the development of plant ideotypes with high yield by improving the plant canopy. The soybean breeding line SS98206SP has shown extremely short petioles in the greenhouse and fields. A new single recessive gene designated as lps3 confers the short petiole trait in SS98206SP. The objectives of this study were to map the short petiole gene in SS98206SP with PCR-based markers. In total, 187 F(2) plants and their F(2:3) families from a cross between the short petiole line SS98206SP and the long petiole cultivar 'Taekwang' along with the two parental lines were evaluated for their petiole lengths in a greenhouse. An SSR marker from each 10-cM section of a consensus soybean map was selected for bulked segregant analysis (BSA) to identify the tentative genomic location of the gene. The BSA technique was useful to localize the gene to a genomic region in the soybean linkage group F (chromosome 13). A linkage map with six SSR and two SNP markers flanking the gene was constructed. We positioned the gene between two SSR markers, Sat_234 and Sct_033, at distances of 8.5 and 3.5 cM from the marker, respectively. The makers flanking the gene (lps3) were located within 3-4 cM of the gene. These markers will be useful for maker-assisted selection in the development of new ideotype soybean plants.

Mapping QTLs for Seminal Root Architecture and Coleoptile Length in Wheat

Root system is important for belowground nutrients acquisition, and is also an important part to respond to drought stress. The purpose of this study was to dissect the genetic basis of seminal root architecture and coleoptile length of wheat by mapping quantitative trait loci (QTLs) of target traits. A doubled haploid (DH) population with 150 lines derived from a cross between two common Chinese wheat varieties Hanxuan 10 and Lumai 14 was used as the plant materials. Gel-chamber was em- ployed to evaluate seminal root architecture traits, including maximum root length (MRL), root number (RN), total root length (TRL), root diameter (RD), root angle (RA), ratio of root dry weight to shoot dry weight (RDW/SDW), and coleoptile length (CL) of seedlings. QTLs for these traits were detected using mixed-model-based composite interval mapping method. A total of 12 additive-effect QTLs and 7 pairs of additive × additive QTLs associated with the target traits were mapped on chromosomes 1A, 1B, 2B, 2D, 3B, 4A, 4D, 5A, 5B, 6A, 7A, and 7B. The phenotypic variation explained by individual additive-effect QTL varied from 5.64% to 12.37%. The additive effects ranged from 0.02 to 8.45. The phenotypic variation explained by each pair of epistatic QTLs varied from 8.70% to 15.90%. The epistatic effects ranged from 0.20 to 7.45. Two QTL clusters for seedling root traits were detected on chromosomes 3B and 7A. These results would be helpful to maker-assisted selection of seminal root architecture and coleoptile.

Screening of IR50 × Rathu Heenati F7 RILs and Identification of SSR Markers Linked to Brown Planthopper (Nilaparvata lugens Stål) Resistance in Rice (Oryza sativa L.)

Brown planthopper (Nilaparvata lugens Stål) is one of the major insect pests of rice. A Sri Lankan indica rice cultivar Rathu Heenati was found to be resistant to all biotypes of the brown planthopper. In the present study, a total of 268 F(7) RILs of IR50 and Rathu Heenati were phenotyped for their level of resistance against BPH by the standard seedbox screening test (SSST) in the greenhouse. A total of 53 SSR primers mapped on the chromosome 3 were used to screen the polymorphism between the parents IR50 and Rathu Heenati, out of which eleven were found to be polymorphic between IR50 and Rathu Heenati. The eleven primers that have shown polymorphism between the IR50 and Rathu Heenati parents were genotyped in a set of five resistant RILs and five susceptible RILs along with the parents for co-segregation analysis. Among the eleven primers, two primers namely RM3180 (18.22 Mb) and RM2453 (20.19 Mb) showed complete co-segregation with resistance. The identification of SSR markers linked with BPH resistant could be used for the maker assisted selection (MAS) program in rice breeding and to map the resistant genes on rice chromosomes for further gene cloning.