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The p21 region of human chromosome 9 is thought to contain a gene (MLM) involved in genetic susceptibility to melanoma and a gene or genes that influence progression of certain other tumors. Genomic clones that span a large region in 9p21 surrounding the presumptive tumor suppressor gene(s) have been isolated. A set of sequence-tagged sites in this region has been developed. By using these markers and others previously reported, the 9p21 region has been studied by physical mapping in 84 melanoma cell lines. A putative tumor suppressor gene, perhaps MLM itself, has been localized to a region of less than 40 kb that lies proximal (centromeric) to the α-interferon gene cluster.

Background Improving the overall production of rice with high quality is a major target of breeders. Mining potential yield-related loci have been geared towards developing efficient rice breeding strategies. In this study, one single-locus genome-wide association studies (SL-GWAS) method (MLM) in conjunction with five multi-locus genome-wide association studies (ML-GWAS) approaches (mrMLM, FASTmrMLM, pLARmEB, pKWmEB, and ISIS EM-BLASSO) were conducted in a panel consisting of 529 rice core varieties with 607,201 SNPs. Results A total of 152, 106, 12, 111, and 64 SNPs were detected by the MLM model associated with the five yield-related traits, namely grain length (GL), grain width (GW), grain thickness (GT), thousand-grain weight (TGW), and yield per plant (YPP), respectively. Furthermore, 74 significant quantitative trait nucleotides (QTNs) were presented across at least two ML-GWAS methods to be associated with the above five traits successively. Finally, 20 common QTNs were simultaneously discovered by both SL-GWAS and ML-GWAS methods. Based on genome annotation, gene expression analysis, and previous studies, two candidate key genes ( LOC_Os09g02830 and LOC_Os07g31450 ) were characterized to affect GW and TGW, separately. Conclusions These outcomes will provide an indication for breeding high-yielding rice varieties in the immediate future.

Background Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is a major threat to wheat production and food security worldwide . Breeding stably and durably resistant cultivars is the most effective approach for managing and controlling the disease. The success of FHB resistance breeding relies on identification of an effective resistant germplasm. We conducted a genome-wide association study (GWAS) using the high-density wheat 90 K single nucleotide polymorphism (SNP) assays to better understand the genetic basis of FHB resistance in natural population and identify associated molecular markers. Results The resistance to FHB fungal spread along the rachis (Type II resistance) was evaluated on 171 wheat cultivars in the 2016–2017 (abbr. as 2017) and 2017–2018 (abbr. as 2018) growing seasons. Using Illumina Infinum iSelect 90 K SNP genotyping data, a genome-wide association study (GWAS) identified 26 loci (88 marker-trait associations), which explained 6.65–14.18% of the phenotypic variances. The associated loci distributed across all chromosomes except 2D, 6A, 6D and 7D, with those on chromosomes 1B, 4A, 5D and 7A being detected in both years. New loci for Type II resistance were found on syntenic genomic regions of chromsome 4AL ( QFhb-4AL , 621.85–622.24 Mb) and chromosome 5DL ( QFhb-5DL , 546.09–547.27 Mb) which showed high collinearity in gene content and order. SNP markers wsnp_JD_c4438_5568170 and wsnp_CAP11_c209_198467 of 5D, reported previously linked to a soil-borne wheat mosaic virus (SBWMV) resistance gene, were also associated with FHB resistance in this study. Conclusion The syntenic FHB resistant loci and associated SNP markers identified in this study are valuable for FHB resistance breeding via marker-assisted selection.

Grapes are among the most widely cultivated horticultural crops and have a long history of domestication. They exhibit genetic variation due to natural crossbreeding, bud mutations, and the changing demand for different types of wine and table grapes. Identifying and distinguishing autochthonous grape cultivars is an essential first step in breeding. In this research, an autochthonous grapevine ( Vitis vinifera L.) population was identified using retrotransposon markers called iPBS (Inter primer binding sites), and genetic relationships with other cultivars from Türkiye and Europe were examined. The association between loci and specific traits was determined using GLM (general linear model) and MLM (mixed linear model) analyses. A total of 136 loci were generated by eight iPBS markers, of which 106 were polymorphic. Genotypes and standard cultivars were clustered into three main groups and seven subclusters by the neighbor-joining method. Structure analysis further classified the genotypes and cultivars into seven populations. Molecular variance analysis revealed that most of the variability occurred among individuals. In the association mapping, 36 loci were correlated with quantitative traits in GLM, while 21 were in MLM. The diversity assessments uncovered significant diversity within the autochthonous grape population, even among individuals with the same name. This diversity retains value for breeding research as it allows identifying distinct genotypes with desirable characteristics. The loci identified through both mapping approaches have the potential to serve as functional markers for selecting genotypes with desired traits.

Mesocotyl is an essential organ of rice for pushing buds out of soil and plays a crucial role in seeding emergence and development in direct-seeding. Thus, identify the loci associated with mesocotyl length (ML) could accelerate breeding progresses for direct-seeding cultivation. Mesocotyl elongation was mainly regulated by plant hormones. Although several regions and candidate genes governing ML have been reported, the effects of them in diverse breeding populations were still indistinct. In this study, 281 genes related to plant hormones at the genomic regions associated with ML were selected and evaluated by single-locus mixed linear model (SL-MLM) and multi-locus random-SNP-effect mixed linear model (mr-MLM) in two breeding panels (Trop and Indx) originated from the 3K re-sequence project. Furthermore, superior haplotypes with longer mesocotyl were also identified for marker assisted selection (MAS) breeding. Totally, LOC_Os02g17680 (explained 7.1-8.9% phenotypic variations), LOC_Os04g56950 (8.0%), LOC_Os07g24190 (9.3%) and LOC_Os12g12720 (5.6-8.0%) were identified significantly associated with ML in Trop panel, whereas LOC_Os02g17680 (6.5-7.4%), LOC_Os04g56950 (5.5%), LOC_Os06g24850 (4.8%) and LOC_Os07g40240 (4.8-7.1%) were detected in Indx panel. Among these, LOC_Os02g17680 and LOC_Os04g56950 were identified in both panels. Haplotype analysis for the six significant genes indicated that haplotype distribution of the same gene varies at Trop and Indx panels. Totally, 8 ( LOC_Os02g17680-Hap1 and Hap2 , LOC_Os04g56950-Hap1 , Hap2 and Hap8 , LOC_Os07g24190-Hap3 , LOC_Os12g12720-Hap3 and Hap6 ) and six superior haplotypes ( LOC_Os02g17680-Hap2 , Hap5 and Hap7 , LOC_Os04g56950-Hap4 , LOC_Os06g24850-Hap2 and LOC_Os07g40240-Hap3 ) with higher ML were identified in Trop and Indx panels, respectively. In addition, significant additive effects for ML with more superior haplotypes were identified in both panels. Overall, the 6 significantly associated genes and their superior haplotypes could be used to enhancing ML through MAS breeding and further promote direct-seedling cultivation.

Background The genetic potential of Central African cattle for enhanced productivity remains largely unexplored. The absence of systematic pedigree recording and performance monitoring represent a major obstacle to implementing informed breeding strategies aimed at improving their production. To address this gap, we performed a genome-wide association analysis (GWAS) on a total of 856 animals genotyped with the GGP Bovine 100K array. The analysis focused on identifying genomic regions and candidate genes associated with body traits in a local Zebu (Gudali) and its crossbreed with the European Simmental (Simgud), using mixed linear models (MLM). Results The SNP-based heritability for the four body traits studied varied between 0.23 ± 0.12 for the height at wither (HAW) to 0.44 ± 0.11 for the sacrum height (SH). The genetic correlation ranged from 0.19 ± 0.14 between height at wither and ear length (EL), to 0.81 ± 0.06 between height at wither and sacrum height. For the phenotypic correlations, the ranges were 0.58 ± 0.00 between body length (BL) and ear length to 0.90 ± 0.06 between height at wither and body length. The maximum Pairwise Linkage Disequilibrium (LD), measured as squared correlation coefficient (r 2 ) was 0.465 for Gudali, decreasing by half (0.23) at a distance of 50,708 bp. For the Simgud population the maximum LD was 0.47 halving (0.23) at 99,201 bp. Notably, we observed extended LD patterns across both the Gudali and Simgud genomes, persisting over distances greater than 1 mbp. These features hold significant potential for association analysis studies and genetic improvement initiatives. A total of 52 SNPs were identified has being associated to the considered body traits. These SNPs were mapped within or near 70 candidate genes across the genome. Among them, the ADGRD1 , NDUFAF1 , RTF1 and ITPKA genes exhibited a pleiotropic effect as they were associated with two or more traits. Additionally, LAMTOR5, PCDH9, BCL2, CTIF, BHLHA15, UNC5D, CNTNAP5, TMEM109, TMEM132A , and NOS1AP genes showed direct association with individual body traits. Conclusions This study identified a number of novel loci associated with pathways influencing growth and body traits, disease resistance and immunity, reproduction and milk production. Overall, the identified genes could be considered as candidate genes in any attempt to improve growth, disease resistance and production in tropical cattle raised under extensive management systems. These genes or genomic regions should be prioritized in future cattle breeding programs in Cameroon.

Background Teak ( Tectona grandis L.f.), an important source of tropical timber with immense economic value, is a highly outcrossing forest tree species. 150 unrelated accessions of teak ( Tectona grandis L.f.) plus trees assembled as clones at National Teak Germplasm Bank, Chandrapur, Maharashtra, India was investigated for association mapping of candidate lignin biosynthesis gene ( CAD1 ) and transcription factors ( MYB1 and MYB2 ). Methods and Results The CAD1 , MYB1 and MYB2 were amplified using specifically designed primers. The amplified sequences were then sequenced and genotyped for 112 SNPs/11 indels. We evaluated the association between SNPs and wood density in teak accessions using GLM and MLM statistical models, with Bonferroni correction applied. The teak accessions recorded an average wood density of 416.69 kg.m −3 (CV 4.97%) and comprised of three loosely structured admixed sub-populations (K = 3), containing 72.05% genetic variation within sub-populations with low intragenic LD (0–21% SNP pairs) at P  < 0.05 and high LD decay (33–934 bp) at R 2  = 0.1. GLM and MLM models discounting systematic biases (Q and K matrices) to avoid false discovery revealed five loci at rare variants (MAF 0.003) and three loci at common variants (MAF 0.05) to be significantly ( P  < 0.05) associated with the wood density. However, the stringent Bonferroni correction (4.06–7.04 × 10 –4 ) yielded only a single associated locus (B1485C/A) from exon of MYB1 transcription factor, contributing to about 10.35% phenotypic variation in wood density trait. Conclusion Scored SNP locus (B1485C/A) can be developed as a molecular probe for selection of improved planting stock with proven wood density trait for a large-scale teak plantation.

Low-temperature stress (LTS) is among the major abiotic stresses affecting the geographical distribution and productivity of the most important crops. Understanding the genetic basis of photosynthetic variation under cold stress is necessary for developing more climate-resilient barley cultivars. To that end, we investigated the ability of chlorophyll fluorescence parameters (FVFM, and FVF0) to respond to changes in the maximum quantum yield of Photosystem II photochemistry as an indicator of photosynthetic energy. A panel of 96 barley spring cultivars from different breeding zones of Canada was evaluated for chlorophyll fluorescence-related traits under cold acclimation and freeze shock stresses at different times. Genome-wide association studies (GWAS) were performed using a mixed linear model (MLM). We identified three major and putative genomic regions harboring 52 significant quantitative trait nucleotides (QTNs) on chromosomes 1H, 3H, and 6H for low-temperature tolerance. Functional annotation indicated several QTNs were either within the known or close to genes that play important roles in the photosynthetic metabolites such as abscisic acid (ABA) signaling, hydrolase activity, protein kinase, and transduction of environmental signal transduction at the posttranslational modification levels. These outcomes revealed that barley plants modified their gene expression profile in response to decreasing temperatures resulting in physiological and biochemical modifications. Cold tolerance could influence a long-term adaption of barley in many parts of the world. Since the degree and frequency of LTS vary considerably among production sites. Hence, these results could shed light on potential approaches for improving barley productivity under low-temperature stress.

Sugarcane is an economically important commercial crop which provides raw material for the production of sugar, jaggery, bioethanol, biomass and other by-products. Sugarcane breeding till today heavily relies on conventional breeding approaches which is time consuming, laborious and costly. Integration of marker-assisted selection (MAS) in sugarcane genetic improvement programs for difficult to select traits like sucrose content, resistance to pests and diseases and tolerance to abiotic stresses will accelerate varietal development. In the present study, association mapping approach was used to identify QTLs and genes associated with sucrose and other important yield-contributing traits. A mapping panel of 110 diverse sugarcane genotypes and 148 microsatellite primers were used for structured association mapping study. An optimal subpopulation number (ΔK) of 5 was identified by structure analysis. GWAS analysis using TASSEL identified a total of 110 MTAs which were localized into 27 QTLs by GLM and MLM (Q + K, PC + K) approaches. Among the 24 QTLs sequenced, 12 were able to identify potential candidate genes, viz., starch branching enzyme, starch synthase 4, sugar transporters and G3P-DH related to carbohydrate metabolism and hormone pathway-related genes ethylene insensitive 3-like 1, reversion to ethylene sensitive1-like, and auxin response factor associated to juice quality- and yield-related traits. Six markers, NKS 5_185, SCB 270_144, SCB 370_256, NKS 46_176 and UGSM 648_245, associated with juice quality traits and marker SMC31CUQ_304 associated with NMC were validated and identified as significantly associated to the traits by one-way ANOVA analysis. In conclusion, 24 potential QTLs identified in the present study could be used in sugarcane breeding programs after further validation in larger population. The candidate genes from carbohydrate and hormone response pathway presented in this study could be manipulated with genome editing approaches to further improve sugarcane crop.

Background Proso millet is a highly nutritious cereal considered an essential component of processed foods. It is also recognized with high water-use efficiency as well as short growing seasons. This research was primarily aimed at investigating the genetic diversity among genotypes based on evaluating those important traits proposed in previous researches under both normal and salinity- stress conditions. Use of Amplified fragment length polymorphism (AFLP) molecular markers as well as evaluating the association between markers and the investigated traits under both conditions was also another purpose of this research. Results According to the phenotypic correlation coefficients, the seed yield had the highest correlation with the forage and biological yields under both conditions. By disintegrating those traits investigated under normal and salinity-stress conditions into principal component analysis, it was found that the first four principal components justified more than 59.94 and 62.48% of the whole variance, respectively. The dendrogram obtained by cluster analysis displayed three groups of genotypes under both normal and salinity- stress conditions. Then, association analyses were conducted on 143 proso millet genotypes and 15 agronomic traits as well as 514 polymorphic AFLP markers (out of 866 created bands) generated by 11 primer combinations (out of the initial 20 primer combinations) EcoRI/MseI. The results obtained by mixed linear model (MLM) indicated that under normal conditions, the M14/E10–45 and M14/E10–60 markers had strong associations with seed yield. A similar trend was also observed for M14/E10–45 and M14/E11–44 markers in relation to forage yield. On the other hand, M14/E10–14, M14/E10–64 markers (for seed yield) and M14/E10–64 marker (for forage yield), had significant and stable association in all environments under salinity-stress conditions. Moreover, a number of markers showed considerable associations and stability under both normal and salinity stress conditions. Conclusions According to the analysis of phenotypic data, the wide germplasm of Iranian proso millet has significant variation in terms of measured traits. It can be concluded that markers showing strong associations with traits under salinity-stress conditions are suitable candidates to be used in future marker-assisted selection (MAS) studies to improve salinity-resistance genotypes of Panicum miliaceum in arid and semiarid areas.