Microsatellite Research Articles

The genomic landscape of short tandem repeats in cattle.

Short tandem repeats (STRs) are abundant and have high mutation rates across cattle genomes; however, comprehensive exploration of cattle STRs is needed. Here, we constructed a comprehensive map of 467 553 polymorphic STRs (pSTRs) constructed from 423 cattle genomes representing 59 breeds worldwide. We observed that pSTRs in coding sequences and 5'UTRs (Untranslated Regions) were under strong selective constraints and exhibited a relatively low level of diversity. Furthermore, we found that these pSTRs underwent more contraction than expansion. Population analysis showed a strong positive correlation (R = 1) between pSTR diversity and single nucleotide polymorphic heterozygosity. We also investigated STR differences between taurine and indicine cattle and detected 2301 highly divergent STRs, which might relate to immune, endocrine and neurodevelopmental pathways. In summary, our large-scale study characterizes the spectrum of STRs in cattle, expands the scale of known cattle STR variation and provides novel insights into differences among various cattle subspecies.

Uniparental disomy (UPD) exclusion in embryos following Preimplantation Genetic Testing for Structural Rearrangements (PGT-SR).

Uniparental disomy (UPD) is a genetic condition which both copies of a chromosome are inherited from a single parent, potentially leading to imprinting disorders. This study aimed to assess the integration of Short Tandem Repeat (STR) analysis into Preimplantation Genetic Testing for Structural Rearrangements (PGT-SR) to assess UPD risk and its impact on selecting euploid embryos for embryo transfer in couples with chromosomal translocations involving imprinted chromosomes. This study evaluated three couples carrying balanced chromosomal translocations: 45,XX,der(13;14)(q10;q10), 46,XX,t(10;11)(q22;q13), and 45,XY,der(14;15)(q10;q10). STR analysis was performed on trophectoderm (TE) biopsies after Whole Genome Amplification (WGA) after PGT-SR analysis using parental blood samples to assess UPD risk in euploid embryos. Haplotyping was conducted with five to six STR markers specific to each rearranged chromosome to detect UPD in euploid embryos. Of the four embryos analyzed across the three families, two couples had euploid embryos that tested negative for UPD. These embryos were successfully transferred, resulting in the birth of two healthy children. In the third family, the euploid embryo also tested negative for UPD but failed to implant after transfer, resulting in no pregnancy. Despite its rarity, UPD involving imprinted chromosomes poses significant clinical risks, as seen in disorders such as Prader-Willi syndrome and Angelman syndrome. This study highlights the importance of integrating UPD screening into PGT-SR protocols, to detect both heterodisomic and isodisomic UPD events minimizing the risk of severe genetic disorders. Integrating STR-based UPD screening within PGT-SR workflows is a reliable and cost-effective strategy that enhances embryo selection and mitigates the risk of imprinting disorders. This approach improves reproductive outcomes for families with chromosomal rearrangements, offering a practical advancement in assisted reproduction.

Comparative analysis of Hymenasplenium (Aspleniaceae) chloroplast genomes from China

Hymenasplenium is one of the two genera in the large fern family Aspleniaceae. A previous study explored the molecular phylogeny of this genus using several chloroplast DNA fragments and identified three major clades, one of which is the monophyletic Old World clade with southwestern China as its diversity center. To date, there were only a few studies conducted on chloroplast genomes in Hymenasplenium or Aspleniaceae, limiting the understanding of the plastome features and its role in evolution of this group. Here, we studied the complete chloroplast genomes of 12 Hymenasplenium species covering all four subclades of the Old World clade distributed in China. The length of the Hymenasplenium plastomes ranged from 151,617 to 151,930 bp, and contained 129 genes in total, comprising 87 protein-coding, 34 tRNA, and eight rRNA genes. The GC content ranged from 41.8% to 42.1%. Comparative analyses of the Hymenasplenium chloroplast genomes displayed conserved genomic structure and identical gene arrangement. A total of 1,375 simple sequence repeats and 1,639 large repeats were detected. In addition, we detailed hypervariable regions that can be helpful for further phylogenetic research and species delimitation in Hymenasplenium. Furthermore, we supported phylogenetic relationships among major groups as well as possible cryptic speciation found in previous research in the genus. Our study provides new insights into evolutionary history and basic resources for phylogenetic and taxonomic studies of the genus Hymenasplenium.

Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits

This study aimed to characterize microsatellites in the rabbit genome using an in silico approach and to develop and validate microsatellite markers. Blood samples were collected from 15 Baladi rabbits and 18 New Zealand White (NZW rabbits). The GMATA software was used to define SSRs in the extracted sequences. Twelve primer pairs were used to validate the loci identified and the primers developed. The total number of the detected microsatellite loci overall chromosomes was 1,136,253. The di-nucleotide microsatellite repeats dominated and exceeded 88% of the detected microsatellites in all chromosomes. There were no microsatellites detected in mitochondrial DNA. The highest relative microsatellite abundance was obtained for chromosome 19, followed by 13 and 6. The highest estimated SSR density was obtained for chromosome 14, and the lowest was for mitochondrial DNA, followed by chromosome 13. The polymorphism was 81.63% and 75.51% for Baladi and NZW rabbits, respectively. The number of detected alleles ranged between two and seven alleles/loci, and polymorphic information content was from 35% to 71%. The AMOVA analysis showed that the total variance of all levels of population structure was 15.734. The results definitely confirmed higher genetic diversity in Baladi compared with NZW rabbits.

Genetic Assessment and Positioning of Algerian Barley Landraces with Respect to Landraces from the Middle East and Europe Using RAPD and SSR Markers

Landraces are a critical genetic resource for resilience breeding, offering solutions to prepare agriculture for the challenges posed by climate change. Their efficient utilisation depends on understanding their history and genetic relationships. The current study investigates the phylogenetic relationships of barley landraces from Algeria, varieties from the Near and Middle East, traditional landraces, and modern cultivars from Europe. Using a core set of 33 varieties, including the wild ancestor Hordeum spontaneum from Armenia, genetic diversity was analysed with Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) markers spanning all barley chromosomes. Based on the SSR-based phylogeny, the Algerian varieties are well clustered with those from the Near East, while distinct from the European varieties. The findings from RAPD markers partially support these results. Using exclusively traditional landraces, where a region of origin can be defined, the SSR markers are analysed separately for each chromosome individually, and the resulting clades are represented by the respective region of origin. This strategy resolves qualitative differences in geographic resolution, depending on the chromosome. While marker HvB23D (chromosome 4) separated the wild H. spontaneum from all domesticated genotypes, markers Bmag19 and Hv13GIII (chromosome 3) reveal four distinct geographic clusters (Maghreb, Near and Middle East, West Europe, Central Europe). These biogeographic patterns suggest a model, where divergence of domesticated barley due to human activity interacted with introgression of individual chromosomes from wild barley, yielding adaptive diversity. These biogeographic patterns suggest a model in which the divergence of domesticated barley, driven by human activity, interacts with the introgression of chromosomes from wild barley, resulting in the creation of adaptive genetic diversity. Our research advances our knowledge of barley landraces’ functional genomics and highlights their potential in molecular breeding, particularly for developing resilient varieties suited to diverse environmental conditions.

Genetic diversity of Phalaenopsis spp. orchids based on ISSR (Inter Simple Sequence Repeat) markers

Genus Phalaenopsis is a popular orchid genus known for its large flowers and varied colors. In the wild, the presence of Phalaenopsis is rare, making propagation a necessary effort for conservation. However, research on the diversity of orchids of the genus Phalaenopsis spp has not been widely carried out. This study aims to determine the genetic diversity of orchids of the genus Phalaenopsis spp (P. deliciosa, P. venosa, P. amboinensis, P. amabilis, P bellina, P. violacea) using ISSR markers. The 5 primers used were, UBC-810, UBC-834, UBC-814, UBC-826, and UBC-843. The genetic diversity facts may be used as the basis for plant breeding method. The DNA samples were isolated and then the concentration and purity were measured. DNA amplification of the samples used the PCR (Polymerase Chain Reaction) with 5 ISSR primers. The NTSYS-pc program (Numeral Taxonomic System) version 2.02 was used to evaluate the scoring data, and the results showed up as cluster dendrograms. The results showed that 6 samples of Phalaenopsis spp were divided into 2 clusters, with similarity index values in the range of 30%-81% and genetic diversity in the range of 19%-70%.

Identification and Precise Mapping of PmHSM, a Novel Recessive Powdery Mildew Resistance Allele from Wheat Landrace Heshangmai.

Common wheat (Triticum aestivum L.) is the world's primary food crop, and ensuring its safe production is of utmost importance for global peace and human development. However, the continuous threat of fungal diseases, including Fusarium head scab, rusts, sharp eyespot, and powdery mildew (PM), poses a significant challenge to production. PM caused by Blumeria graminis f. sp. tritici causes substantial yield losses. Heshangmai (HSM), a wheat landrace originating from Sichuan Province, possesses high levels of resistance to PM. A comprehensive study using a large segregating population of a cross between HSM and Ningmaizi119 (NMZ119) revealed a single recessive allele conferring resistance. The gene, provisionally designated PmHSM, was located on the long arm of chromosome 4A (4AL). Molecular marker analysis, a PM response array, and an allelism test indicated that PmHSM is a novel recessive resistance gene that shares an allelic relationship with PmHHXM. Thirteen simple sequence repeat markers were developed using the sequence information of the 4AL region in the Chinese spring reference sequence version 2.1. PmHSM was flanked by the markers Xmp1567 and Xmp1444 at genetic distances of 0.11 and 0.18 cM, respectively, and cosegregated with the markers Xmp1439/Xmp1440/Xmp1442.

Revealing the Dynamic History of Parasitic Plant Plastomes via Structural Characterization, Comparative Analysis, and Phylogenomics

Background: The shift to a parasitic lifestyle in plants often leaves distinct marks on their plastid genomes, given the central role plastids play in photosynthesis. Studying these unique adaptations in parasitic plants is essential for understanding the mechanisms and evolutionary patterns driving plastome reduction in angiosperms. By exploring these changes, we can gain deeper insights into how parasitism reshapes the genomic architecture of plants. Method: This study analyzed and compared the plastomes of 113 parasitic plants from different families. Results: The Orobanchaceae family (hemiparasitic plants) displayed the largest plastome size, while Apodanthaceae exhibited the shortest. Additionally, Orobanchaceae showcased little to no gene loss in their plastomes. However, holoparasitic species typically had reduced plastome sizes. Convolvulaceae exhibited significantly reduced plastome sizes due to high gene loss, and Apodanthaceae retained only a few genes. Gene divergence among different families was also investigated, and rps15, rps18, and rpl33 in Orobanchaceae; accD and ycf1 in Convolvulaceae; atpF and ccsA in Loranthaceae; and rpl32 in Santalaceae showed greater divergence. Additionally, Orobanchaceae had the highest numbers of all repeat types, whereas Loranthaceae and Convolvulaceae exhibited the lowest repeat numbers. Similarly, more simple sequence repeats were reported in Loranthaceae and Santalaceae. Our phylogenetic analysis also uncovered a distinct clade comprising Loranthaceae, with a single Schoepfiaceae species clustering nearby. Contrary to expectations, parasitic and hemiparasitic plants formed mixed groupings instead of segregating into separate clades. Conclusions: These findings offer insights into parasitic plants’ evolutionary relationships, revealing shared and divergent genomic features across diverse lineages.

Assessment of genetic diversity and population structure analysis in Himalayan garlic genotypes from Sikkim using SSR markers.

Garlic (Allium sativum L.) is an important crop with significant medicinal and culinary uses. Understanding the genetic diversity and population structure of Himalayan garlic genotypes from Sikkim is crucial for effective breeding and conservation efforts. This study aims to analyze the genetic diversity among 60 Himalayan garlic genotypes collected from various altitudinal locations of Sikkim, India, using 27 Simple Sequence Repeats (SSR) markers. The genetic diversity was assessed using SSR markers, which revealed substantial variation among the genotypes. The number of alleles (Na) ranged from 1.13 to 2.00, while the major allele frequency (MAF) varied from 0.672 to 0.963. The observed heterozygosity (Ho) ranged from 0.0667 to 0.475, indicating moderate genetic diversity. Population structure analysis using STRUCTURE software grouped the genotypes into three distinct sub-populations, suggesting genetic differentiation not solely based on leaf morphology. Analysis of Molecular Variance (AMOVA) showed that genetic variation was more significant among individuals within populations (41%) than among populations (16%). UPGMA dendrogram and Principal Coordinates Analysis (PCoA) further confirmed the genetic relationships among the genotypes. This study reveals significant genetic diversity among Himalayan garlic genotypes from Sikkim, with clear genetic differentiation observed within and between populations. The results highlight the importance of both leaf morphology types and genetic structure in understanding the genetic basis of phenotypic variation in garlic. The finding provides valuable insights for future breeding programs and conservation strategies, emphasizing the need to consider morphological and genetic data for effective germplasm management and improvement of garlic cultivars.

Genetic diversity, morphological characteristics and virulence of Stemphylium species causing tomato leaf spot disease in Uruguay

AbstractTomato leaf spot, caused by the ascomycete fungi Stemphylium spp., including S. lycopersici, S. solani and S. vesicarium, is a severe threat to tomato production worldwide. In Uruguay, the disease has become more prevalent in both field and greenhouse production systems in recent years, primarily due to the use of susceptible tomato varieties. This study focuses on the identification, morphological characteristics, genetic diversity and virulence of Stemphylium isolates responsible for leaf spot in Uruguay's major tomato‐producing regions. Phylogenetic analysis using partial sequences of the rDNA internal transcribed spacer (ITS) and glyceraldehyde‐3‐phosphate dehydrogenase (gpd) genes showed that S. lycopersici is the predominant pathogen, with 33 isolates identified, whereas only three isolates were classified as S. vesicarium. Genetic diversity analysis using inter simple sequence repeat (ISSR) markers identified two main clusters of S. lycopersici isolates that correlate with distinct geographical regions. Cultural and morphological characteristics of S. lycopersici varied significantly and pathogenicity assays revealed a broad spectrum of virulence among S. lycopersici isolates, with some isolates causing extensive necrosis and others showing minimal disease lesions. S. lycopersici primarily penetrates plant tissues through stomata and trichomes, and hyphae proliferate both within and on plant tissues, causing chlorosis and necrosis. Infected tissues exhibit alterations in cell wall composition associated with the incorporation of phenolic compounds. This is the first report characterizing various isolates of S. lycopersici and S. vesicarium responsible for tomato leaf spot in Uruguay.

Physiological response of diverse maize genotypes to heat stress and simple sequence repeats markers-based genotyping in Rawalpindi, Punjab Pakistan

The current study was designed to observe the response of maize genotypes under high-temperature stress conditions and to check their diversity using simple sequence repeats (SSR) markers in in-vitro conditions. Maize genotypes (n=10) were subjected to heat stress at ~45 °C for 72 h after growing into young seedlings. Their physiological responses were determined by measuring the changes in proline content (PC), chlorophyll content (CC), cell membrane stability (CMS), relative water content (RWC) and osmotic potential (Ψπ). The analysed data disclosed significant differences (P ≤ 0.01) among all the characters. Comparison between control and heat-treated genotypes depicted a notable increase in PC, Ψπ while a decrease in CC, RWC and CMS index in heat-treated plants. Maize genotypes viz. NCEV-1230, NARC-4, HN Gold and OPV-20 performed better under heat stress and also showed a strong genetic relationship for similarity index in dendrogram based on selected SSR markers related to abiotic stress tolerance. This study is beneficial for understanding the physiological behaviour of maize plants under heat stress and for further genetic studies on maize to select heat-tolerant lines for breeding programs

Assessment of Genetic Diversity for MYMV Resistance in Mungbean [Vigna radiata (L.) Wilczek] using SSR Markers

Background: Mung bean (Vigna radiata L.) is among the most significant edible legume crops and consumed in various parts of the world. Among different biotic factors, mungbean yellow mosaic virus (MYMV) affects this crop. The objective of the present investigation was to assess genetic variability among mungbean genotypes for MYMV resistance using simple sequence repeat markers. Methods: The present research was conducted to assess the genetic diversity among selected mungbean genotypes from field screening of 303 genotypes with an emphasis on resistance against MYMV. The field screening was done at Seed Breeding Farm, College of Agriculture, JNKVV, Jabalpur, Madhya Pradesh during summer 2022, kharif 2022 and summer 2023. Thirty SSR markers have been utilized to measure genetic variation among the 32 studied genotypes. Result: Marker MB-SSR033 stands out as the most informative locus with the greatest PIC and gene diversity value. The cluster analysis, classified the 32 genotypes into two major groups and maximum distance was noted between PDM 139 and IC 314523. The SSR markers CEDG293 (10.14%) and DMBSSR008 (9.11%) were found considerably linked to MYMV resistance. Harnessing multiple sources of resistance gives a good possibility to boost the resistance and production of mungbean cultivars.

Genome-Wide Analysis of the NBS-LRR Gene Family and SSR Molecular Markers Development in Solanaceae

The Solanaceae family occupies a significant position, and the study of resistance genes within this family is extremely valuable. Therefore, our goal is to examine disease resistance genes based on the high-quality representative genomes of Solanaceae crops, and to develop corresponding Simple Sequence Repeat (SSR) molecular markers. Among nine representative Solanaceae species, we identified 819 NBS-LRR genes, which were further divided into 583 CC-NBS-LRR (CNL), 54 RPW8-NBS-LRR (RNL), and 182 TIR-NBS-LRR (TNL) genes. Whole genome duplication (WGD) has played a very important role in the expansion of NBS-LRR genes in Solanaceae crops. Gene structure analysis showed the striking similarity in the conserved motifs of NBS-LRR genes, which suggests a common ancestral origin, followed by evolutionary differentiation and amplification. Gene clustering and events like rearrangement within the NBS-LRR family contribute to their scattered chromosomal distribution. Our findings reveal that the majority of NBS-LRR family genes across all examined species predominantly localize to chromosomal termini. The analysis indicates the significant impact of the most recent whole genome triplication (WGT) on the NBS-LRR family genes. Moreover, we constructed Protein–Protein Interaction (PPI) networks for all 819 NBS-LRR genes, identifying 3820 potential PPI pairs. Notably, 97 genes displayed clear interactive relationships, highlighting their potential role in disease resistance processes. A total of 22,226 SSRs were detected from all genes of nine Solanaceae species. Among these SSRs, we screened 43 NBS-LRR-associated SSRs. Our study lays the foundation for further exploration into SSR development and genetic mapping related to disease resistance in Solanaceae species.

Comparative chloroplast genomes analysis of nine Primulina (Gesneriaceae) rare species, from karst region of southwest China

Guizhou Province is one of the most important karst regions of southwest China, with 22 Primulina species. These species are highly habitat-specialized and dependent on the soils of the karst region, and many inter-species classifications are unclear. Therefore, studying the chloroplast genomes and estimating the divergence times of there species can not only provide a better understanding of interspecific relationships but also help to know the species speciation and divergence in the karst environment. So, we sequenced and assembled the chloroplast genomes of nine Primulina species (including six endemic species of Guizhou) and conducted chloroplast genome comparison analysis and phylogenetic study. The chloroplast genome structures of the nine Primulina species were quadripartite with total lengths of 152,869–153,364 base pairs (bp) and GC content of 37.55–37.64%. There are 132 functional genes annotated, respectively. A total of 375 simple sequence repeats and 375 interspersed nuclear elements were identified. The 30 highly preferred codons identified were used at similar frequencies in different species, respectively. A phylogenetic tree constructed on the basis of the 38 chloroplast genomes showed that Primulina species form a monophyletic group. Eleven mutational hotspot regions that could serve as potential molecular markers were identified, of which two regions near the 3′ and 5′ ends of the ycf1 gene were of appropriate size and can serve as molecular markers for phylogenetic studies of Primulina. The results of molecular clock analyses indicate that the three major branches of Primulina begin to diverge in the Miocene, and the number of species proliferated in the Pliocene and Pleistocene. Most of the species of Primulina in Guizhou Province were formed in the Pleistocene and rapidly diverged within a short period of time. This research study enriches the genetic resource information of Primulina and deepens the understanding of the phylogenetic relationships of the genus.

Touch DNA viability on various substrates from different shedder levels

BACKGROUND Touch DNA samples are frequently discovered at crime scenes, including those found at the scene, on the victim, with the suspect, or on objects related to the incident. This study aimed to investigate 3 key factors affecting touch DNA samples: the characteristics person that shed the DNA, surfaces variants where the DNA was deposited, and different sampling methods effectiveness that influence DNA quantity, quality, and detection. METHODS 9 participants grouped into high, intermediate, and low shedder levels simultaneously tied 2 types of ropes, non-porous and porous. The first person will hold a rope for 5 min then pass it to the second person to hold on the same spot for another 5 min. DNA was collected from each rope using the double swab and tape-lift method, extracted, and quantified using real-time polymerase chain reaction (PCR). Touch DNA profile at 20 short tandem repeat loci was amplified in PCR system and detected on capillary electrophoresis. RESULTS Type of substrate (p = 0.97) or sampling method (p = 0.053) used for touch DNA collection did not significantly impact the DNA yield or profiling outcomes. A notable difference (p<0.001) was found in DNA quantity between high, intermediate, and low shedders, regardless of the substrate or method used. CONCLUSIONS Individual shedder level has a greater influence on the results of touch DNA analysis regarding the DNA quantity and profiling quality than substrate type and sample procedure.

Establishment and characterization of the novel myxofibrosarcoma cell line, SMU-MFS.

Myxofibrosarcoma (MFS) is one of the most common soft-tissue sarcomas in elderly patients. Owing to the limited efficacy of chemotherapy and radiotherapy, complete resection is the only available curative treatment. Therefore, developing novel therapies for MFS is important to improve clinical outcomes. Herein, a novel MFS cell line, namely SMU-MFS, was established to better understand the biologic characteristics of MFS and develop new therapies. A tissue sample from the surgically resected tumor tissue of a 56-year-old patient with a tumor was subjected to primary culture. The cell line was established and authenticated by assessing the short tandem repeats of DNA microsatellites. The monolayer cultures of SMU-MFS cells exhibited constant growth, spheroid formation, and invasive capacity. Furthermore, the cells exhibited low chemosensitivity to doxorubicin, eribulin, and pazopanib, which are used to inhibit metastatic progression. In addition, of the four mice inoculated with SMU-MFS cells, tumors developed in two mice after 8weeks. Altogether, the findings of this study suggest that the SMU-MFS cell line can be a useful tool for investigating MFS development and evaluating novel therapeutic agents.

Genetic Identity and Diversity of Loggerhead Sea Turtles in the Central Mediterranean Sea

Background: The conservation of loggerhead sea turtles (Caretta caretta) in the central Mediterranean benefits from an in-depth understanding of its population genetic structure and diversity. Methods: This study, therefore, investigates C. caretta in Maltese waters by genetically analysing 63 specimens collected through strandings and in-water sampling, using mitochondrial DNA control region and microsatellites. Additionally, the two nests detected in Malta in 2023 were analysed for the same markers. Results: Mitochondrial data identified 10 haplotypes, with mixed stock analyses tracing 87.5% of the specimens to Mediterranean origins, primarily from Libyan rookeries, with contributions from Lebanon, Israel and Turkey. Three Atlantic haplotypes were identified in six specimens, with CC-A17.1 linking central Mediterranean foraging individuals to rookeries in Cape Verde. Five of these six Atlantic haplotype records were from recently sampled individuals (2022–2023), possibly indicating a recent eastward expansion of Atlantic haplotypes into the Mediterranean. Bayesian clustering (K = 2) of microsatellite data using haplotypes as priori revealed similar proportions for clusters across most specimens, except for three specimens with Atlantic haplotypes CC-A1.1 and CC-A1.3, which exhibited distinct patterns. The two nests examined here displayed Mediterranean haplotypes, with nuclear DNA matching the predominant Mediterranean profiles found in foraging individuals, suggesting that local clutches originated from Mediterranean parents. Conclusions: Increasing nesting activity on Maltese beaches and this archipelago’s geographical position highlight the need for ongoing genetic monitoring to track changes in genetic diversity and develop conservation strategies that support the effective protection of this species and its habitats.

Analysis of genetic diversity in the free-pollinated F1 population of Hippophae rhamnoides L. subsp. mongolica ‘Shenqiuhong’ via simple sequence repeat markers

Analysis of genetic diversity in the free-pollinated F1 population of Hippophae rhamnoides L. subsp. mongolica ‘Shenqiuhong’ via simple sequence repeat markers

Genetic dissection of flour whiteness through genome-wide association analysis in common wheat (Triticum aestivum L.)

The color of flour products has an important influence on consumer acceptance. Flour color is largely determined and measured by the index of flour whiteness (FW) in China. In this study, an association population comprising 207 wheat (Triticum aestivum) accessions originating from seven countries was used for dissection of FW-related genetic loci through genome-wide association analysis. Six quantitative trait loci (QTLs) significantly associated with FW were identified, accounting for 7.87%–16.53% of the total phenotypic variation. Four KASP markers were developed from single-nucleotide polymorphisms associated with the QTLs QFW.HAAS-1AS, QFW.HAAS-1BL, QFW.HAAS-5AL, and QFW.HAAS-7AL. The phytoene synthase-encoding gene TraesCS7A03G1357000 (TaPsyA1) was identified as a candidate gene for QFW.HAAS-7AL. Two allelic variants of TaPsyA1 (designated PsyA1-a and PsyA1-b) were differentiated on the basis of a 37bp insertion/deletion polymorphism in the second intron. PsyA1-b included the 37bp insertion, which led to a translational frameshift in the gene and was associated with higher FW. The PsyA1-a allele lacked the 37bp insertion and was classified into two haplotypes according to the number of repeated ‘TC’ units in a simple sequence repeat in the promoter region. Of the two PsyA1-a haplotypes, the Type 1 haplotype conferred higher FW, flour brightness, and flour redness, and lower yellow pigment content and flour yellowness. The KASP markers and PsyA1 polymorphic markers developed in the present study are suitable for use in molecular marker-assisted selection for improvement of wheat FW.

Sensitivity and Specificity of Chimerism Tests in Predicting Leukemia Relapse Using Increasing Mixed Chimerism

Chimerism test was evaluated to predict leukemia relapse. Increasing mixed chimerism (IMC), defined as recipient increase ≥0.1% in peripheral blood total cell chimerism, was used as a surrogate of disease activity. Combination of quantitative PCR and short-tandem repeat method was applied to achieve high assay sensitivity. Total of 184 patients received stem cell transplant for acute myeloid leukemia (N = 110), acute lymphocytic leukemia (N = 41), myelodysplastic syndrome (N = 30), and 2389 chimerism tests (median follow-up, 1054 days). Sixty-six patients relapsed, and 118 patients did not. Cumulative incidence of relapse increased after 1 IMC or ≥2 consecutive IMCs (hazard ratios, 9.9 and 44.4, respectively). Predicted percentage relapse by day 30 after IMC was 0% (0 IMC), 10% (1 IMC), and 40% (≥2 IMCs). The last chimerism results before relapse detected IMC in 57 of 66 relapsed patients (sensitivity, 86.4%). Nine patients had no IMC before relapse (false negative) because of rapidly evolving relapse (N = 4) or extramural relapse (N = 5). In 118 patients without relapse, 158 of 1873 tests detected IMC (false positive, 8.4%; specificity, 91.6%). The false-positive rates increased with higher percentage recipient T-cell chimerism levels, indicating T-cell contamination as a cause. Chimerism monitoring predicts relapse. However, caution must be taken for false-positive or false-negative IMCs. T-cell removal can improve chimerism test specificity in patients with mixed T-cell chimerism.