High-density Genetic Linkage Research Articles

Mapping Quantitative Trait Loci Related to Spike Traits Using a RILs Population of Yanda 1817 × Beinong 6 in Wheat ( Triticum aestivum L.)

Spike length(SL), grain number per spike(GNS), and grain weight per spike(GWS) are important spike traits associated with yield in wheat. In this study, quantitative trait loci(QTLs) for spike traits were mapped using an available high-density SNP and SSR genetic linkage map developed from a recombinant inbred line(RIL) population of Yanda 1817 × Beinong 6. Using phenotypic data on two locations(Beijing and Shijiazhuang) in two years(2011–2012 and 2012–2013 growing seasons), 29 QTLs for SL, GNS and GWS were detected by inclusive composite interval mapping(ICIM)(LOD ≥ 2.5). Among which, 10 QTLs for spike length were mapped on chromosomes 1B, 2D, 3A, 3B, 4A, 5A, 5B, 6A, and 7D with phenotypic variations ranging from 2.96% to 9.63%. A stable and major QTL associated with SL, QSl.cau-4A.2, was detected in all the environments with phenotypic variations ranging from 5.89% to 9.62%. Eight QTLs for GNS were found on chromosomes 1A, 3A, 3D, 4A, and 5B with phenotypic variations from 4.06% to 11.17%. However, they were all environments sensitive and detected in a single environment. Eleven QTLs for GWS were mapped on chromosomes 1A, 1B, 2A, 2D, 3A, 4D, 5A, 5B, and 6B with phenotypic variations ranging from 2.79% to 16.12%. The QTL QGws.cau-6B.2 was identified in three environments and the favorable allele was contributed by Beinong 6. The stable QTLs on chromosomes 3A, 4A, 6B, and 7D identified in this study may serve as target sites in marker-assisted selection of spike related traits in wheat breeding program.

A major quantitative trait locus conferring adult plant partial resistance to crown rust in oat.

BackgroundCrown rust, caused by Puccinia coronata f. sp. avenae, is the most important disease of oat worldwide. Adult plant resistance (APR), based upon partial resistance, has proven to be a durable rust management strategy in other cereal rust pathosystems. The crown rust APR in the oat line MN841801 has been effective for more than 30 years. The genetic basis of this APR was studied under field conditions in three recombinant inbred line (RIL) populations: 1) AC Assiniboia/MN841801, 2) AC Medallion/MN841801, and 3) Makuru/MN841801. The populations were evaluated for crown rust resistance with the crown rust isolate CR251 (race BRBB) in multiple environments. The 6 K oat and 90 K wheat Illumina Infinium single nucleotide polymorphism (SNP) arrays were used for genotyping the AC Assiniboia/MN841801 population. KASP assays were designed for selected SNPs and genotyped on the other two populations.ResultsThis study reports a high density genetic linkage map constructed with oat and wheat SNP markers in the AC Assiniboia/MN841801 RIL population. Most wheat SNPs were monomorphic in the oat population. However the polymorphic wheat SNPs could be scored accurately and integrated well into the linkage map. A major quantitative trait locus (QTL) on oat chromosome 14D, designated QPc.crc-14D, explained up to 76% of the APR phenotypic variance. This QTL is flanked by two SNP markers, GMI_GBS_90753 and GMI_ES14_c1439_83. QPc.crc-14D was validated in the populations AC Medallion/MN841801 and Makuru/MN841801.ConclusionsWe report the first APR QTL in oat with a large and consistent effect. QPc.crc-14D was statistically significant in all environments tested in each of the three oat populations. QPc.crc-14D is a suitable candidate for use in marker-assisted breeding and also an excellent target for map-based cloning. This is also the first study to use the 90 K wheat Infinium SNP array on oat for marker development and comparative mapping. The Infinium SNP array is a useful tool for saturating oat maps with markers. Synteny with wheat suggests that QPc.crc-14D is orthologous with the stripe rust APR gene Yr16 in wheat.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-014-0250-2) contains supplementary material, which is available to authorized users.

A High-Density SNP Map for Accurate Mapping of Seed Fibre QTL in Brassica napus L

A high density genetic linkage map for the complex allotetraploid crop species Brassica napus (oilseed rape) was constructed in a late-generation recombinant inbred line (RIL) population, using genome-wide single nucleotide polymorphism (SNP) markers assayed by the Brassica 60 K Infinium BeadChip Array. The linkage map contains 9164 SNP markers covering 1832.9 cM. 1232 bins account for 7648 of the markers. A subset of 2795 SNP markers, with an average distance of 0.66 cM between adjacent markers, was applied for QTL mapping of seed colour and the cell wall fiber components acid detergent lignin (ADL), cellulose and hemicellulose. After phenotypic analyses across four different environments a total of 11 QTL were detected for seed colour and fiber traits. The high-density map considerably improved QTL resolution compared to the previous low-density maps. A previously identified major QTL with very high effects on seed colour and ADL was pinpointed to a narrow genome interval on chromosome A09, while a minor QTL explaining 8.1% to 14.1% of variation for ADL was detected on chromosome C05. Five and three QTL accounting for 4.7% to 21.9% and 7.3% to 16.9% of the phenotypic variation for cellulose and hemicellulose, respectively, were also detected. To our knowledge this is the first description of QTL for seed cellulose and hemicellulose in B. napus, representing interesting new targets for improving oil content. The high density SNP genetic map enables navigation from interesting B. napus QTL to Brassica genome sequences, giving useful new information for understanding the genetics of key seed quality traits in rapeseed.

A SNP-Based Genetic Linkage Map of Soybean Using the SoyS - NP6K Illumina Infinium BeadChip Genotyping Array

This study reports a high density genetic linkage map based on the ‘Maryland 96-5722’ by ‘Spencer’ recombinant inbred line (RIL) population of soybean [Glycine max (L.) Merr.] and constructed exclusively with single nucleotide polymorphism (SNP) markers. The Illumina Infinium SoySNP6K BeadChip genotyping array produced 5,376 SNPs in the mapping population, with a 96.75% success rate. Significant level of goodness-of-fit for each locus was tested based on the observed vs. expected ratio (1:1). Out of 5,376 markers, 1,465 SNPs fit the 1:1 segregation rate having ≤20% missing data plus heterozygosity among the RILs. Among this 1,456 just 657 were polymorphic between the parents DNAs tested. These 657 SNPs were mapped using the JoinMap 4.0 software and 550 SNPs were distributed on 16 linkage groups (LGs) among the 20 chromosomes of the soybean genome. The total map length was just 201.57 centiMorgans (cM) with an average marker density of 0.37 cM. This is one of the high density SNP-based genetic linkage maps of soybean that will be used by the scientific community to map quantitative trait loci (QTL) and identify candidate genes for important agronomic traits in soybean.

Correction: Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth-Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

Correction: Construction of a High-Density Microsatellite Genetic Linkage Map and Mapping of Sexual and Growth-Related Traits in Half-Smooth Tongue Sole (Cynoglossus semilaevis)

Quantitative Trait Loci Associated with Moisture, Protein, and Oil Content in Soybean [Glycine max (L.) Merr.

The objectives of this study were to detect quantitative trait loci (QTL) for moisture, protein, and oil content in soybean grown in two plant density environments. Soybean recombinant inbred lines (RIL), obtained from a cross between cultivars PI 438489B and Hamilton, were used. Thirty one linkage groups were obtained from high density genetic linkage maps constructed by 1,536 Universal Soy Linkage Panel 1.0 of single nucleotide polymorphisms (SNP) markers. For the lines cultivated in higher plant density (25 cm row space), ten QTLs were mapped in A2, B2, C2, D1a, M and O linkage groups for moisture, protein, and oil. Two QTLs for moisture, two QTLs for protein and six QTLs for oil explained 0.09, 15.36 and 3.54% of the phenotypic variation of moisture, protein, and oil respectively. For the lines cultivated in lower density (50 cm row space), three QTLs for each of moisture and protein were mapped in linkage groups A2, C1, D1b, L and O; QTLs for moisture and protein explained 0.96 and 10.63% of the phenotypic variation respectively. These QTL will facilitate the implementation of MAS for moisture, protein and oil content in soybean-breeding programs.

A High Resolution Genetic Map Anchoring Scaffolds of the Sequenced Watermelon Genome

As part of our ongoing efforts to sequence and map the watermelon (Citrullus spp.) genome, we have constructed a high density genetic linkage map. The map positioned 234 watermelon genome sequence scaffolds (an average size of 1.41 Mb) that cover about 330 Mb and account for 93.5% of the 353 Mb of the assembled genomic sequences of the elite Chinese watermelon line 97103 (Citrullus lanatus var. lanatus). The genetic map was constructed using an F8 population of 103 recombinant inbred lines (RILs). The RILs are derived from a cross between the line 97103 and the United States Plant Introduction (PI) 296341-FR (C. lanatus var. citroides) that contains resistance to fusarium wilt (races 0, 1, and 2). The genetic map consists of eleven linkage groups that include 698 simple sequence repeat (SSR), 219 insertion-deletion (InDel) and 36 structure variation (SV) markers and spans ∼800 cM with a mean marker interval of 0.8 cM. Using fluorescent in situ hybridization (FISH) with 11 BACs that produced chromosome-specifc signals, we have depicted watermelon chromosomes that correspond to the eleven linkage groups constructed in this study. The high resolution genetic map developed here should be a useful platform for the assembly of the watermelon genome, for the development of sequence-based markers used in breeding programs, and for the identification of genes associated with important agricultural traits.

A transcriptome map of perennial ryegrass (Lolium perenne L.)

BackgroundSingle nucleotide polymorphisms (SNPs) are increasingly becoming the DNA marker system of choice due to their prevalence in the genome and their ability to be used in highly multiplexed genotyping assays. Although needed in high numbers for genome-wide marker profiles and genomics-assisted breeding, a surprisingly low number of validated SNPs are currently available for perennial ryegrass.ResultsA perennial ryegrass unigene set representing 9,399 genes was used as a reference for the assembly of 802,156 high quality reads generated by 454 transcriptome sequencing and for in silico SNP discovery. Out of more than 15,433 SNPs in 1,778 unigenes fulfilling highly stringent assembly and detection parameters, a total of 768 SNP markers were selected for GoldenGate genotyping in 184 individuals of the perennial ryegrass mapping population VrnA, a population being previously evaluated for important agronomic traits. A total of 592 (77%) of the SNPs tested were successfully called with a cluster separation above 0.9. Of these, 509 (86%) genic SNP markers segregated in the VrnA mapping population, out of which 495 were assigned to map positions. The genetic linkage map presented here comprises a total of 838 DNA markers (767 gene-derived markers) and spans 750 centi Mogan (cM) with an average marker interval distance of less than 0.9 cM. Moreover, it locates 732 expressed genes involved in a broad range of molecular functions of different biological processes in the perennial ryegrass genome.ConclusionsHere, we present an efficient approach of using next generation sequencing (NGS) data for SNP discovery, and the successful design of a 768-plex Illumina GoldenGate genotyping assay in a complex genome. The ryegrass SNPs along with the corresponding transcribed sequences represent a milestone in the establishment of genetic and genomics resources available for this species and constitute a further step towards molecular breeding strategies. Moreover, the high density genetic linkage map predominantly based on gene-associated DNA markers provides an important tool for the assignment of candidate genes to quantitative trait loci (QTL), functional genomics and the integration of genetic and physical maps in perennial ryegrass, one of the most important temperate grassland species.

On the road to a high density genetic linkage map of wheat chromosome 5A

On the road to a high density genetic linkage map of wheat chromosome 5A

Germplasm and breeding research of tea plant based on DNA marker approaches

Tea is the most popular non-alcoholic and healthy beverage worldwide. Tea production contributes greatly to the economy and provides job opportunities for many countries in Asia and Africa. Meanwhile, the germplasm of tea, with a huge potential for the future of the whole tea industry, is presently one of the most valuable and fundamental materials for tea breeding and tea biotechnology. DNA molecular markers have been proven to be robust and valuable approaches in the studies of genetic diversity and variation, molecular identification, molecular phylogenetics, genetic stability and integrity of tea germplasm and the genetic linkage map for breeding of tea. In this paper, a brief description of the molecular marker studies of tea has been summarized. The purpose is to provide an effective way of undertaking a massive tea germplasm appraisal and evaluation, to develop new applicable and cheap DNA markers, to establish a high density genetic linkage map and analyze the agronomically important QTLs and, finally, to facilitate the markers assisted early selection and shorten breeding procedures in tea.

Detection and validation of single feature polymorphisms in cowpea (Vigna unguiculata L. Walp) using a soybean genome array

BackgroundCowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.ResultsHere we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max) genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.ConclusionWe conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.

Hitchhiking Effect Mapping: A New Approach for Discovering Agronomic Important Genes

Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep (haplotype block) could be detected after draft genome scanning (genome typing) with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci (or QTLs) even the favored alleles (genes) in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.

Genetic mapping reveals a single major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

Bacterial wilt caused by Xanthomonas translucens pv. graminis (Xtg) is a major disease of economically important forage crops such as ryegrasses and fescues. Targeted breeding based on seedling inoculation has resulted in cultivars with considerable levels of resistance. However, the mechanisms of inheritance of resistance are poorly understood and further breeding progress is difficult to obtain. This study aimed to assess the relevance of the seedling screening in the glasshouse for adult plant resistance in the field and to investigate genetic control of resistance to bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.). A mapping population consisting of 306 F1 individuals was established and resistance to bacterial wilt was assessed in glasshouse and field experiments. Highly correlated data (r = 0.67-0.77, P < 0.01) between trial locations demonstrated the suitability of glasshouse screens for phenotypic selection. Analysis of quantitative trait loci (QTL) based on a high density genetic linkage map consisting of 368 amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers revealed a single major QTL on linkage group (LG) 4 explaining 67% of the total phenotypic variance (Vp). In addition, a minor QTL was observed on LG 5. Field experiments confirmed the major QTL on LG 4 to explain 43% (in 2004) to 84% (in 2005) of Vp and also revealed additional minor QTLs on LG 1, LG 4 and LG 6. The identified QTLs and the closely linked markers represent important targets for marker-assisted selection of Italian ryegrass.

Restriction Fragment Length Polymorphisms (RFLPS) and Crop Improvement

SUMMARYRestriction fragment length polymorphisms (RFLPs) are genetic markers based on cloned molecules of DNA. Using RFLPs, scientists can construct high density genetic linkage maps and locate economically important genes. Once a gene for a valuable trait has been mapped with RFLPs, desirable genotypes can be selected using RFLPs rather than scoring for the trait itself. This is important when a trait is recessive, difficult to score, or obscured by other characters. RFLPs are particularly valuable in mapping genes controlling complex polygenic characters, including those fundamental to crop improvement. The first RFLP maps were developed in crop species primarily important in temperate countries. Now RFLP maps for major tropical and sub-tropical crop species are also being developed.