Kompetitive Allele-specific Polymerase Chain Research Articles

Variation in Acetyl-CoA Carboxylase Beta Gene and Its Effect on Carcass and Meat Traits in Gannan Yaks.

Acetyl-CoA carboxylase beta (ACACB) is a functional candidate gene that impacts fat deposition. In the present study, we sequenced exon 37-intron 37, exon 46-intron 46, and intron 47 of yak ACACB using hybrid pool sequencing to search for variants and genotyped the gene in 593 Gannan yaks via Kompetitive allele-specific polymerase chain (KASP) reaction to determine the effect of ACACB variants on carcass and meat quality traits. Seven single nucleotide polymorphisms were detected in three regions. Eight effective haplotypes and ten diplotypes were constructed. Among them, a missense variation g.50421 A > G was identified in exon 37 of ACACB, resulting in an amino acid shift from serine to glycine. Correlation analysis revealed that this variation was associated with the cooking loss rate and yak carcass weight (p = 0.024 and 0.012, respectively). The presence of haplotypes H5 and H6 decreased Warner-Bratzler shear force (p = 0.049 and 0.006, respectively), whereas that of haplotypes H3 and H4 increased cooking loss rate and eye muscle area (p = 0.004 and 0.034, respectively). Moreover, the presence of haplotype H8 decreased the drip loss rate (p = 0.019). The presence of one and two copies of haplotypes H1 and H8 decreased the drip loss rate (p = 0.028 and 0.004, respectively). However, haplotype H1 did not decrease hot carcass weight (p = 0.011), whereas H3 increased the cooking loss rate (p = 0.007). The presence of one and two copies of haplotype H6 decreased Warner-Bratzler shear force (p = 0.014). The findings of the present study suggest that genetic variations in ACACB can be a preferable biomarker for improving yak meat quality.

Introgression of sharp eyespot resistance from Dasypyrum villosum chromosome 2VL into bread wheat

Wheat sharp eyespot, a stem disease caused by the soilborne fungus Rhizoctonia cerealis van der Hoeven, has become a threat to wheat production worldwide. Exploiting resistance resources from wild relatives of wheat is a promising strategy for controlling this disease. In this study, a new wheat–Dasypyrum villosum T2DS·2V#4L translocation line in the background of Chinese Spring (CS) showed stable resistance to R. cerealis. Introgression of the T2DS·2V#4L chromosome into wheat cultivar Aikang 58 by backcrossing produced a marked increase in sharp eyespot resistance in NIL-T2DS·2V#4L in comparison with NIL-T2DS·2DL, and no detrimental effects of 2V#4L on agronomic traits were observed in the BC2F2, BC2F2:3, and BC2F2:4 generations. Flow-sorted sequencing of 2V#4L yielded 384.3 Mb of assembled sequence, and 8836 genes were predicted of which 6154 had orthologs in at least one of the 2AL, 2BL, and 2DL arms of CS, whereas 1549 genes were unique to 2V#4L. About 100,000 SNPs were detected in genes of 2V#4L and 2DL in 10 sequenced bread wheat cultivars. A Kompetitive Allele Specific Polymerase chain reaction and 30 conserved ortholog sequence markers were developed to trace the 2V#4L chromatin in wheat backgrounds. T2DS·2V#4L compensating translocation lines represent novel germplasm with sharp eyespot resistance and the markers will allow rapid detection in breeding programs.

Application of three methods in water‐saving wheat breeding

AbstractAt present, water shortage seriously affects wheat production in many parts of the world, and to solve this problem, water‐saving wheat breeding is an important research domain. The objective of this study was to evaluate water‐saving index (WSI), yield factors, and KASP (kompetitive allele specific polymerase chain reaction) markers in water‐saving wheat breeding carried out in Hengshui region, China. The result showed as follows: (1) The new index WSI could better indicate the water‐saving performance, including the yield potential and the stability of different wheat cultivars under water limited condition (WL). (2) Referring to the degree of heat stress (D) in that year, selecting one of the three yield factors as the focus will improve the breeding efficiency of water‐saving wheat cultivars. With the increase of the D within a certain range, high water‐saving wheat cultivars showed a high grain weight (GW) under WL. Meanwhile with the decreasing of D value, high water‐saving wheat cultivars showed high spike number under WL. (3) KASP aggregation breeding will significantly improve the efficiency of water‐saving breeding. The combination with the highest effective rate of selecting water‐saving varieties carried GS5‐2334‐SNP and Dreb_SNP favorable alleles, and GW2‐6B‐1709SNP, TaMoc‐2433, and 1fehw with adverse alleles, whereas GS5‐2334‐SNP and GW2‐6B‐1709SNP that related to GW were useful markers for water‐saving breeding. These results improved our knowledge on the usage of WSI, yield factors, and KASP markers on water‐saving wheat breeding.

Effects of Genes, Lifestyles, and Noise Kurtosis on Noise-Induced Hearing Loss.

To explore the association of lifestyles, caspase gene (CASP), and noise kurtosis with noise-induced hearing loss (NIHL). Three hundred seven NIHL individuals and 307 matched controls from factories in Chinese factories participated in this case-control study. Age, sex, noise exposure, exfoliated oral mucosa cells, and lifestyles of participants were gathered by the authors. The single nucleotide polymorphisms (SNPs) were genotyped using the Kompetitive Allele Specific polymerase chain reaction (KASP) method. The risk of NIHL was higher for people who worked in the complex noise environment than for people exposed to steady noise environment (adjusted: OR = 1.806, P = 0.002). Smoking and regular earphone use increased the risk of NIHL (adjusted: OR = 1.486, P = 0.038). The GG genotype of the recessive model and G allele in rs1049216, together with the TT genotype of the recessive model in rs6948 decreased the NIHL risk (adjusted: OR = 0.659, P = 0.017). Oppositely, the AA genotype of additive model in rs12415607 had a higher NIHL risk (adjusted: OR = 1.804, P = 0.024). In the additive models, there was a positive interaction between noise kurtosis and CASP3 polymorphisms (RERI = 1.294, P = 0.013; RERI = 1.198, P = 0.031). Noise kurtosis, three SNPs (rs1049216, rs6948, and rs12415607), smoking and earphone use were found to be related to NIHL, and there was a positive interaction between noise kurtosis and CASP3. Results from this study can be used to prevent and detect NIHL and for genetic testing.

Genetic mapping and confirmation of the Rdm3 locus underlying resistance to southern stem canker in soybean

AbstractSouthern stem canker (SSC) in soybean [Glycine max (L.) Merrill], caused by the fungal pathogen Diaporthe aspalathi, is a major disease in the southern United States. It can cause up to 80% yield loss in severely infected fields. Plant introduction (PI) 398469, a Maturity Group VI soybean accession from South Korea, is one of six known sources of resistance to SSC. To determine the genetics of the resistance provided by PI 398469, F2:3 and F5‐derived recombinant inbred line (RIL) populations were developed from a cross with the susceptible breeding line G81‐2057. Both populations were phenotyped in the greenhouse using a modified toothpick method. The SSC‐resistant and susceptible DNA bulks consisting of 20 resistant and 18 susceptible families were created from the F2:3 population and genotyped using the Infinium SoySNP50K BeadChips for a bulked segregant analysis (BSA). Based on BSA results, 22 Kompetitive allele specific polymerase chain reaction (KASP) markers were designed to genotype the RIL population. Quantitative trait locus (QTL) analysis identified qRdm_14, on chromosome (Chr) 14 with an R2 of 62%. Linkage mapping in the F2:3 population confirmed the presence of a QTL on Chr 14. F5‐derived RILs derived from G81‐2057 × Crockett were phenotyped for SSC resistance and genotyped with the KASP markers to examine the relationship between Rdm3 from Crockett and qRdm_14 from PI 398469. Both PI 398469 and Crockett carried realleles at the Rdm3 locus for resistance to SSC. The QTL and KASP marker information could be used to screen breeding lines for resistance to SSC.

Whole-genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut.

Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed-size improvement as one of the most important objectives of groundnut breeding programs globally. Marker-based early generation selection can accelerate the process of breeding for developing large-seeded varieties. In this context, we deployed the quantitative trait locus-sequencing (QTL-seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4-389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9-95.1% genome coverage and 8.34-9.29× average read depth. The analysis of sequencing data using QTL-seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single-nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large-seeded groundnut varieties.

Diagnostic KASP markers differentiate Vanilla planifolia, V. odorata, V. pompona, and their hybrids using leaf or cured pod tissues.

Vanilla is a globally important spice crop used in a variety of food, cosmetic, and pharmaceutical products. V. planifolia is the primary commercial species with V. x tahitensis also permissible for food use. Other aromatic species, including V. pompona, are used for food throughout Central and South America. Supply chain complexity hinders the vanilla bean industry and can lead to false claims of genetic and geographical origins to obtain higher prices. Beans of some species can be differentiated by experienced buyers, but hybrids and morphological differences caused by environmental variability or disease would best be resolved by diagnostic tests. METHODS ANDRESULTS: Kompetitive Allele Specific Polymerase Chain Reaction is a widely used molecular marker that can genotype single nucleotide polymorphisms efficiently and inexpensively. Assays were designed to differentiate V. planifolia, V. x tahitensis, and V. pompona using publicly available vanilla genomics data. Ten KASP assays on chromosomes 1 through 7, the ITS region, and plastid-encoded rbcL gene successfully differentiated V. planifolia, V. odorata, and V. x tahitensis. Additional KASP assays on chromosomes 1 through 4, the ITS region, and rbcL gene successfully differentiated V. planifolia and V. pompona. Further, a method for extracting KASP-quality DNA from cured vanilla bean seeds was developed and successfully differentiated V. planifolia, V. odorata, V. x tahitensis, V. pompona, and their hybrids. The methods and results from this study can be used to identify interspecific hybrids, ensure the authenticity of cured vanilla beans, and reduce abuse within the vanilla supply chain.

Development and validation of diagnostic markers for the wheat Fusarium head blight resistance gene Fhb7

AbstractFusarium head blight (FHB), mainly incited by Fusarium graminearum Schwabe, has caused great losses in grain yield and quality of wheat globally. Fhb7, a gene with a major effect on FHB resistance, was recently cloned and shown to be a GST encoding glutathione S‐transferase. Fhb7 originated from the 7E chromosome of Thinopyrum ponticum and confers broad resistance to Fusarium species. However, high‐throughput diagnostic markers are not available for wider deployment of Fhb7 in breeding programs. To develop such DNA markers for high‐throughput screening of Fhb7, we designed two kompetitive allele specific polymerase chain reaction (KASP) markers (Fhb7‐KASP1 and Fhb7‐KASP2) based on the promoter and coding sequences of GST homologs and tested their cosegregation with Fhb7 FHB resistance in a recombinant inbred population. As a validation of their usefulness in marker‐assisted selection in breeding programs, Fhb7‐KASP1 and Fhb7‐KASP2 were shown to be diagnostic for Fhb7 status in a set of RWG34‐near‐isogenic lines (NILs) and a natural winter wheat population (RGON2020). Haplotype analysis of Thinopyrum accessions using the two markers and GST homolog sequences identified only six accessions with the Fhb7 resistance marker alleles and the Hap I‐R haplotype, and five of them were cytologically confirmed to be Th. ponticum, the species in which Fhb7 was originally identified. The development of the diagnostic markers in this study will facilitate the deployment of Fhb7 in wheat breeding programs to improve FHB resistance.

Adult plant leaf rust resistance QTL derived from wheat line CI13227 maps to chromosomes 2AL, 4BS, and 7AL.

The winter wheat (Triticum aestivum L.) line CI13227 has been characterized as having adult plant resistance to leaf rust caused by Puccinia triticina Eriks (Pt). Line CI13227 was crossed with the susceptible spring wheat 'Thatcher' (Tc) and a Tc*2/CI13227 F6 line with adult plant leaf rust resistance designated as 411A was derived. Line 411A was crossed with Tc to develop an F6 recombinant inbred line (RIL) population. The parents and 120 F6 lines were assessed for leaf rust severity at the flag leaf stage in five field plot tests from 2011 through 2015 and were genotyped for single-nucleotide polymorphism (SNP) markers with the Illumina iSelect 90K wheat bead array. A total of 2,384 SNP markers segregated among the RILs. Completely linked SNPs were removed, and 474 markers that covered 2,605 centimorgans (cM) were used for linkage map construction. Quantitative trait loci (QTL) on chromosome 2AL with logarithm of odds (LOD) values 2.34-7.88, on chromosome 4BS with LOD values 1.35- 4.66, and on chromosome 7AL with LOD values 2.92-7.81 were associated with significant reduction in leaf rust severity in the field plot tests. Recombinant inbred lines that had combinations of two or three of the QTL had significantly lower leaf rust severity than RILs that lacked any resistance QTL. Kompetitive allele specific polymerase chain reaction (KASP) markers were developed for the SNPs that were closely linked with the three QTL to facilitate marker-based selection of the leaf rust resistance in breeding programs.

Development of single nucleotide polymorphism‐based functional molecular markers from the Lr22a gene sequence in wheat (Triticum aestivum)

AbstractThe adult‐plant leaf rust resistant gene Lr22a confers broadly effective resistance against the fungal pathogen Puccinia triticina Eriks. (Pt) in wheat that has not been extensively utilized in wheat cultivars. The objective of this study was to develop robust functional molecular markers using the Lr22a gene sequence to facilitate integration of Lr22a in breeding programmes. The Lr22a coding sequence was used to identify isolated SNPs and four kompetitive allele specific polymerase chain reaction (PCR) (KASP) markers were developed. For marker testing, a F2:3 population was developed by crossing a near‐isogenic line RL4495 (Lr22a carrier) with Thatcher and phenotyped with Pt race TDBJ and genotyped with a 90K iSelect SNP array, four KASP markers and two SSR markers. A linkage map of chromosome arm 2DS that included Lr22a was constructed. The KASP markers co‐segregated with Lr22a and were validated for cross‐applicability on a panel of wheat lines. KASP markers Kwh636, Kwh637 and Kwh638 reliably detected the presence or absence of Lr22a. The markers developed in this study will facilitate Lr22a selection in breeding programmes.

Identification and Characterisation of Stripe Rust Resistance Genes Yr66 and Yr67 in Wheat Cultivar VL Gehun 892

Wheat cultivar VL Gehun 892 has shown a high level of resistance against Australian Puccinia striiformis f. sp. tritici (Pst) pathotypes. In this study, it was crossed with Westonia, a susceptible wheat cultivar, and digenic segregation was observed in the derived population against Pst pathotype 134 E16A+Yr17+Yr27+. Single-gene recombinant inbred line (RIL) populations were developed from F3 families (VL Gehun 892/Westonia#1 and VLGehun 892/Westonia#4) that showed monogenic segregations with two distinct phenotypes. Single-gene segregation against Pst pathotype 134 E16A+Yr17+Yr27+ was confirmed in both F6 RIL populations. Bulked segregant analysis using a 90K Infinium SNP array placed YrVL1 in the short arm of chromosome 3D and YrVL2 in the long arm of chromosome 7B. Kompetitive allele specific polymerase chain reaction (KASP) assays were developed for the SNPs linked with YrVL1 and YrVL2 and were mapped onto the respective populations. KASP_48179 (0.6 cM proximal) and KASP_18087 (2.1 cM distal) flanked YrVL1, whereas YrVL2 was mapped between KASP_37096 (1.2 cM proximal) and KASP_2239 (3.6 cM distal). Based on their pathotypic specificities, map locations, and stages of expression, YrVL1 and YrVL2 were demonstrated to be unique loci and named Yr66 and Yr67, respectively. Markers linked with these genes showed more than 85% polymorphism when tested on a set of 89 Australian cultivars and hence could be used for the marker-assisted selection of these genes in wheat breeding programs, following checks of parental polymorphisms.

Identification of resistance loci toward Phytophthora sojae in South Korean soybean plant introductions 407974B and 424487B

AbstractPhytophthora root and stem rot is a major constraint to soybean [Glycine max (L.) Merr.] production worldwide. Deployment of single dominant Resistance to Phytophthora sojae (Rps) genes are an effective management strategy for this disease. However, due to increasing diversity in P. sojae populations for pathotype, new effective Rps genes are needed. Two recombinant inbred line (RIL) populations, each derived from a cross with Williams (susceptible) and resistant accessions PI 407974B and PI 424487B, were evaluated for resistance with one or more P. sojae pathotypes: OH1 (vir 7), OH4 (vir 1a, 1c, 7), OH7 (vir 1a, 3a, 3c, 4, 5, 6, 7), OH25 (vir 1a, 1b, 1c, 1k, 7), and 1.S.1.1 (1a, 1b, 1k, 2, 3a, 3c, 4, 5, 6, 7, 8). Molecular maps were assembled with BARCSoySNP6K BeadChip, simple‐sequence repeat, and Kompetitive Allele Specific polymerase chain reaction markers. A total of three Rps loci were mapped, one near Rps1 on Chromosome 3 and two near Rps4/6 on chromosome 18. Quantitative trait loci and straight linkage maps confirmed the loci. Resistance to P. sojae pathotypes 1.S.1.1 and/or OH7 was mapped to Chromosome 3 in the PI 407974B RIL population. PI 407974B and PI 424487B RIL populations have Rps loci on chromosome 18 toward OH4 and OH25, respectively, which are near the Rps4/6 region. Although these PIs may have novel Rps genes/alleles and could assist in the deployment and pyramiding of resistance against P. sojae, care should be taken because these may condition defense reactions to some P. sojae pathotypes but not to all.

Registration of ‘White Pearl’ great northern common bean cultivar with upright plant architecture and high yield

AbstractGreat northern common bean (Phaseolus vulgaris L.) cultivar ‘White Pearl’ (Reg. no. CV‐343, PI 698189) was developed by the dry bean breeding program at the University of Nebraska and released in 2018. It was bred specifically for adaptation to western Nebraska growing conditions and for upright plant architecture, high yield, and enhanced resistance to bean rust, common bacterial blight (CBB), and Bean common mosaic virus (BCMV). Seed yield of White Pearl was comparable and slightly higher than other great northern cultivars in on‐station trials conducted in Nebraska and did not differ significantly in yield from ‘Aries’ and ‘Matterhorn’ in regional trials. Seed size (100‐seed weight) of White Pearl was larger than ‘Marquis’, ‘Orion’, ‘Gemini’, ‘Beryl‐R’, and Aries in trials grown in Nebraska. White Pearl carries the sequence characterized amplified region (SCAR) marker SAP6 linked to a major quantitative trait locus (QTL) for resistance to CBB. White Pearl had a CBB disease rating of 6.0 (intermediate) under field conditions at the Scottsbluff and Mitchell Ag Labs in 2020. White Pearl also has the Ur‐3 gene for resistance to bean rust and carries the SS68 Kompetitive Allele Specific polymerase chain reaction (KASP) and SK14 SCAR markers linked to the Ur‐3 locus. It also contains the single dominant hypersensitive I gene that confers resistance to all non‐necrotic strains of BCMV and the SW13 SCAR marker linked to the I gene. White Pearl has bright white seed, blooms 46 d after planting, and is a midseason bean, maturing 89 d after planting.

Development and Validation of KASP Assays for the Genotyping of Racing Performance-Associated Single Nucleotide Polymorphisms in Pigeons.

Pigeon racing’s recent upturn in popularity can be attributed in part to the huge prize money involved in these competitions. As such, methods to select pigeons with desirable genetic characteristics for racing or for selective breeding have also been gaining more interest. Polymerase chain reaction—restriction fragment length polymorphism (PCR-RFLP) for genotyping-specific genes is one of the most commonly used molecular techniques, which can be costly, laborious and time consuming. The present study reports the development of an alternative genotyping method that employs Kompetitive Allele Specific Polymerase Chain Reaction (KASP) technology with specifically designed primers to detect previously reported racing performance-associated polymorphisms within the LDHA, MTYCB, and DRD4 genes. To validate, KASP assays and PCR-RFLP assays results from 107 samples genotyped for each of the genes were compared and the results showed perfect (100%) agreement of both methods. The developed KASP assays present an alternative rapid, reliable, and cost-effective method to identify polymorphisms in pigeons.

Precise mapping of QTL for Hessian fly resistance in the hard winter wheat cultivar 'Overland'.

A major QTL for Hessian fly resistance was precisely mapped to a 2.32 Mb region on chromosome 3B of the US hard winter wheat cultivar 'Overland'. The Hessian fly (HF, Mayetiola destructor) is a destructive insect pest of wheat in the USA and worldwide. Deploying HF-resistant cultivars is the most effective and economical approach to control this insect pest. A population of 186 recombinant inbred lines (RILs) was developed from 'Overland' × 'Overley' and phenotyped for responses to HF attack using the HF biotype 'Great Plains'. A high-density genetic linkage map was constructed using 1,576 single nucleotide polymorphism (SNP)markers generated by genotyping-by-sequencing(GBS). Two quantitative trait loci (QTLs) with a significant epistatic effect on HF resistance were mapped to chromosomes 3B (QHf.hwwg-3B) and 7A (QHf.hwwg-7A) in Overland, which are located in similar chromosome regions as found for H35 and H36 in the cultivar 'SD06165', respectively. QHf.hwwg-3B showed a much larger effect on HF resistance than QHf.hwwg-7A. Five and four GBS-SNPs, respectively, in the QHf.hwwg-3B and QHf.hwwg-7A QTL intervals were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. QHf.hwwg-3B was precisely mapped to a 2.32Mb interval (2,479,314-4,799,538bp) using near-isogenic lines (NILs) and RILs that have recombination within the QTL interval. The US winter wheat accessions carrying contrasting alleles at KASP markers KASP-3B4525164, KASP-7A47772047 and KASP-7A65090410 showed significant difference in HF resistance. The combination of the two KASP markers KASP-3B3797431 and KASP-3B4525164 is near-diagnostic for the detection ofQHf.hwwg-3B in a US winter wheat panel and can be potentially used for screening the QTL in breeding programs.

Identification of a major QTL for Hessian fly resistance in wheat cultivar ‘Chokwang’

The Hessian fly (HF, Mayetiola destructor) is one of the destructive pests of wheat (Triticum aestivum L.) worldwide. Resistant cultivars can effectively minimize wheat damage due to this insect pest. To identify new quantitative trait loci (QTL) for HF resistance, a population of recombinant inbred lines (RILs) was developed from a cross between the HF-resistant wheat cultivar ‘Chokwang’ and susceptible wheat ‘Ning 7840’, and phenotyped for responses to HF attack. A linkage map was constructed using 1147 single nucleotide polymorphism (SNP) markers generated from genotyping-by-sequencing (GBS). One major QTL, QHf.hwwg-6BS, for HF-resistance was identified on chromosome arm 6BS, which explained up to 84.0% of the phenotypic variation and was contributed by Chokwang. Two RILs showed recombination in the candidate interval of QHf.hwwg-6BS, which delimited QHf.hwwg-6BS to a 4.75 Mb physical interval between 6,028,601 bp and 10,779,424 bp on chromosome arm 6BS of IWGSC Chinese Spring reference genome RefSeq v2.0. Seven GBS-SNPs in the candidate interval were converted into Kompetitive allele specific polymerase chain reaction (KASP) markers. Two of them, KASP-6B112698 and KASP-6B7901215, were validated in a U.S. winter wheat panel. KASP-6B112698 was nearly diagnostic, thus can be used to screen QHf.hwwg-6BS and pyramid it with other resistance genes in breeding programs.

SNP-based assessment of genetic purity and diversity in maize hybrid breeding.

Assessment of genetic purity of parental inbred lines and their resultant F1 hybrids is an essential quality control check in maize hybrid breeding, variety release and seed production. In this study, genetic purity, parent-offspring relationship and diversity among the inbred lines were assessed using 92 single-nucleotide polymorphism (SNP) markers. A total of 188 maize genotypes, comprising of 26 inbred lines, four doubled haploid (DH) lines and 158 single-cross maize hybrids were investigated in this study using Kompetitive Allele Specific Polymerase Chain Reaction (KASP) genotyping assays. The bi-allelic data was analyzed for genetic purity and diversity parameters using GenAlex software. The SNP markers were highly polymorphic and 90% had polymorphic information content (PIC) values of > 0.3. Pairwise genetic distances among the lines ranged from 0.05 to 0.56, indicating a high level of dissimilarity among the inbred lines. A maximum genetic distance of (0.56) was observed between inbred lines CKDHL0089 and CML443 while the lowest (0.05) was between I-42 and I-40. The majority (67%) of the inbred lines studied were genetically pure with residual heterozygosity of <5%, while only 33% had heterozygosity levels of >5%. Inbred lines, which were not pure, require purification through further inbreeding. Cluster analysis partitioned the lines into three distinct genetic clusters with the potential to contribute new beneficial alleles to the maize breeding program. Out of the 68 hybrids (43%) that passed the parent-offspring test, seven hybrids namely; SCHP29, SCHP95, SCHP94, SCHP134, SCHP44, SCHP114 and SCHP126, were selected as potential candidates for further evaluation and release due to their outstanding yield performance.

Genetic Mapping and Validation of Loci for Kernel-Related Traits in Wheat (Triticum aestivum L.).

Kernel size (KS) and kernel weight play a key role in wheat yield. Phenotypic data from six environments and a Wheat55K single-nucleotide polymorphism array–based constructed genetic linkage map from a recombinant inbred line population derived from the cross between the wheat line 20828 and the line SY95-71 were used to identify quantitative trait locus (QTL) for kernel length (KL), kernel width (KW), kernel thickness (KT), thousand-kernel weight (TKW), kernel length–width ratio (LWR), KS, and factor form density (FFD). The results showed that 65 QTLs associated with kernel traits were detected, of which the major QTLs QKL.sicau-2SY-1B, QKW.sicau-2SY-6D, QKT.sicau-2SY-2D, and QTKW.sicau-2SY-2D, QLWR.sicau-2SY-6D, QKS.sicau-2SY-1B/2D/6D, and QFFD.sicau-2SY-2D controlling KL, KW, KT, TKW, LWR, KS, and FFD, and identified in multiple environments, respectively. They were located on chromosomes 1BL, 2DL, and 6DS and formed three QTL clusters. Comparison of genetic and physical interval suggested that only QKL.sicau-2SY-1B located on chromosome 1BL was likely a novel QTL. A Kompetitive Allele Specific Polymerase chain reaction (KASP) marker, KASP-AX-109379070, closely linked to this novel QTL was developed and used to successfully confirm its effect in two different genetic populations and three variety panels consisting of 272 Chinese wheat landraces, 300 Chinese wheat cultivars most from the Yellow and Huai River Valley wheat region, and 165 Sichuan wheat cultivars. The relationships between kernel traits and other agronomic traits were detected and discussed. A few predicted genes involved in regulation of kernel growth and development were identified in the intervals of these identified major QTL. Taken together, these stable and major QTLs provide valuable information for understanding the genetic composition of kernel yield and provide the basis for molecular marker–assisted breeding.

Correlation between the Polymorphism of Coagulation-Related Genes and Lower Extremity Deep Venous Thrombosis.

Objective To investigate the correlation between the polymorphism of 4 coagulation-related genes, rs1799963 （coagulation factor V gene Leiden）, rs6025 （prothrombin gene G20210A）, rs1042579 （thrombomodulin protein gene c.1418C>T） and rs1801131 （methylenetetrahydroflate reductase gene） and lower extremity deep venous thrombosis （LEDVT）. Methods The 4 genotypes mentioned above of 150 LEDVT patients and 153 healthy controls were detected by the kompetitive allele specific polymerase chain reaction （KASP）, then related blood biochemical indicators were collected, binary Logistic regression was established to screen the independent risk factors of LEDVT, and the correlation between polymorphism of 4 coagulation-related genes and LEDVT and its indicators under different genetic modes after adjusting confounding factors were analyzed. Results Five variables, D-dimer, fibrinogen degradation product, homocysteine, sex and age might be the risk factors of LEDVT. These variables were put into 4 genetic inheritance models, and adjusted in binary Logistic regression. The results suggested that the mutations of rs1042579 were correlated with LEDVT under dominant inheritance mode. Conclusion The gene polymorphism of rs1799963, rs6025 and rs1801131 has no significant correlation with the formation of LEDVT. The gene polymorphism of rs1042579 plays a role under dominant inheritance mode, and might be an independent risk factor for formation of LEDVT.

Identification and validation of Fusarium head blight resistance QTL in the U.S. soft red winter wheat cultivar ‘Jamestown’

AbstractUse of genetic resistance is one of the most important strategies to manage the devastating disease Fusarium head blight (FHB) in wheat. Numerous quantitative trait loci (QTL) having varying effects on reducing FHB and the mycotoxin deoxynivalenol (DON) accumulation have been reported from Asian, European, or distant sources such as wild relatives of wheat (Triticum aestivum L.). However, coming from nonadapted backgrounds, the incorporation of such QTL into regional breeding programs has often resulted in the simultaneous transfer of other undesirable traits. Therefore, it is important to identify, characterize, and deploy sources of genetic resistance that do not suffer from poor adaptability and/or linkage drag. In the present work, QTL associated with FHB resistance in a high‐yielding, moderately resistant soft red winter wheat cultivar ‘Jamestown’ were mapped and validated. The QTL mapping was done using a recombinant inbred line (RIL) population of Pioneer ‘25R47’ × Jamestown having 186 individuals. Phenotyping over 2 yr at three locations, and genotyping using the 90K single nucleotide polymorphism (SNP) platform identified two new QTL, named QFHB.vt‐1B.1 and QFHB.vt‐1B.2, on the chromosome 1B long arm. The QTL contributed to FHB incidence, FHB severity, Fusarium‐damaged kernels, and DON content. Independent mapping of these QTL using two additional RIL populations of FG95195 × Jamestown (170 RILs) and Jamestown × LA97113UC‐124 (77 RILs) validated their stability and effectiveness in different genetic backgrounds. Kompetitive allele specific polymerase chain reaction (KASP) assays were developed using linked SNPs for marker‐assisted selection of the QTL. These QTL are being used in breeding programs to develop FHB‐resistant, high‐yielding varieties.