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Biofortification of provitamin A in maize is an attractive and sustainable remedy to the problem of vitamin A deficiency in developing countries. The utilization of molecular markers represents a promising avenue to facilitate the development of provitamin A (PVA)-enriched maize varieties. We screened 752 diverse tropical yellow/orange maize lines using kompetitive allele-specific PCR (KASP) makers to validate the use of KASP markers in PVA maize breeding. To this end, a total of 161 yellow/orange inbred lines, selected from among the 752 lines, were evaluated for their endosperm PVA and other carotenoid compounds levels in two separate trials composed of 63 and 98 inbred lines in 2020 and 2021, respectively. Significant differences (p < 0.001) were observed among the yellow maize inbred lines studied for all carotenoid profiles. An inbred line TZMI1017, introduced by the International Institute of Tropical Agriculture (IITA) showed the highest level of PVA (12.99 µg/g) and ß-carotene (12.08 µg/g). The molecular screening showed 43 yellow maize inbred lines carrying at least three of the favorable alleles of the KASP markers. TZMI1017 inbred line also carried the favorable alleles of almost all markers. In addition, nine locally developed inbred lines had medium to high PVA concentrations varying from 5.11 µg/g to 10.76 µg/g and harbored the favorable alleles of all the KASP PVA markers. Association analysis between molecular markers and PVA content variation in the yellow/orange maize inbred lines did not reveal a significant, predictable correlation. Further investigation is warranted to elucidate the underlying genetic architecture of the PVA content in this germplasm. However, we recommend strategic utilization of the maize-inbred lines with higher PVA content to enhance the PVA profile of the breeding program's germplasm.

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Janus kinase 2 (JAK2) plays a critical role in myoblast proliferation and fat deposition in animals. Our previous RNA-Seq analyses identified a close association between the JAK2 gene and muscle development. To date, research delving into the relationship between the JAK2 gene and growth traits has been sparse. In this study, we sought to investigate the relationship between novel mutations within the JAK2 gene and goat growth traits. Herein, two novel InDel (Insertion/Deletion) polymorphisms within the JAK2 gene were detected in 548 goats, and only two genotypes were designated as ID (Insertion/Deletion) and DD (Deletion/Deletion). The results indicate that the two InDels, the del19008 locus in intron 2 and del72416 InDel in intron 6, showed significant associations with growth traits (p < 0.05). Compared to Nubian and Jianzhou Daer goats, the del72416 locus displayed a more pronounced effect in the Fuqing breed group. In the Nubian breed (NB) group, both InDels showed a marked influence on body height (BH). There were strong linkages observed for these two InDels between the Fuqing (FQ) and Jianzhou (JZ) populations. The DD-ID diplotype was associated with inferior growth traits in chest width (ChW) and cannon circumference (CaC) in the FQ goats compared to the other diplotypes. In the NB population, the DD-DD diplotype exhibited a marked negative impact on BH and HuWI (hucklebone width index), in contrast to the other diplotypes. In summary, our findings suggest that the two InDel polymorphisms within the JAK2 gene could serve as valuable molecular markers for enhancing goat growth traits in breeding programs.

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Rice, a critical staple on a global scale, faces escalating challenges in yield preservation due to the rising prevalence of abiotic and biotic stressors, exacerbated by frequent climatic fluctuations in recent years. Moreover, the scorching climate prevalent in the rice-growing regions of South China poses obstacles to the cultivation of good-quality, heavy-grain varieties. Addressing this dilemma requires the development of resilient varieties capable of withstanding multiple stress factors. To achieve this objective, our study employed the broad-spectrum blast-resistant line Digu, the brown planthopper (BPH)-resistant line ASD7, and the heavy-grain backbone restorer lines Fuhui838 (FH838) and Shuhui527 (SH527) as parental materials for hybridization and multiple crossings. The incorporation of molecular markers facilitated the rapid pyramiding of six target genes (Pi5, Pita, Pid2, Pid3, Bph2, and Wxb ). Through a comprehensive evaluation encompassing blast resistance, BPH resistance, cold tolerance, grain appearance, and quality, alongside agronomic trait selection, a promising restorer line, Guihui5501 (GH5501), was successfully developed. It demonstrated broad-spectrum resistance to blast, exhibiting a resistance frequency of 77.33% against 75 artificially inoculated isolates, moderate resistance to BPH (3.78 grade), strong cold tolerance during the seedling stage (1.80 grade), and characteristics of heavy grains (1,000-grain weight reaching 35.64 g) with good grain quality. The primary rice quality parameters for GH5501, with the exception of alkali spreading value, either met or exceeded the second-grade national standard for premium edible rice varieties, signifying a significant advancement in the production of good-quality heavy-grain varieties in the southern rice-growing regions. Utilizing GH5501, a hybrid combination named Nayou5501, characterized by high yield, good quality, and resistance to multiple stresses, was bred and received approval as a rice variety in Guangxi in 2021. Furthermore, genomic analysis with gene chips revealed that GH5501 possessed an additional 20 exceptional alleles, such as NRT1.1B for efficient nitrogen utilization, SKC1 for salt tolerance, and STV11 for resistance to rice stripe virus. Consequently, the restorer line GH5501 could serve as a valuable resource for the subsequent breeding of high-yielding, good-quality, and stress-tolerant hybrid rice varieties.

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BACKGROUND: Among the Citrus species, lemon (Citrus limon Burm f.) is one of the most affected by the two-spotted spider mite (Tetranychus urticae Koch). Moreover, chemical control is hampered by the mite's ability to develop genetic resistance against acaricides. In this context, the identification of the genetic basis of the host resistance could represent a sustainable strategy for spider mite control. In the present study, a marker-trait association analysis was performed on a lemon population employing an association mapping approach. An inter-specific full-sib population composed of 109 accessions was phenotyped through a detached-leaf assays performed in modified Huffaker cells. Those individuals, complemented with two inter-specific segregating populations, were genotyped using a target-sequencing approach called SPET (Single Primer Enrichment Technology), the resulting SNPs were employed for the generation of an integrated genetic map. RESULTS: The percentage of damaged area in the full-sib population showed a quantitative distribution with values ranging from 0.36 to 9.67%. A total of 47,298 SNPs were selected for an association mapping study and a significant marker linked with resistance to spider mite was detected on linkage group 5. In silico gene annotation of the QTL interval enabled the detection of 13 genes involved in immune response to biotic and abiotic stress. Gene expression analysis showed an over expression of the gene encoding for the ethylene-responsive transcription factor ERF098-like, already characterized in Arabidopsis and in rice for its involvement in defense response. CONCLUSION: The identification of a molecular marker linked to the resistance to spider mite attack can pave the way for the development of marker-assisted breeding plan for the development of novel selection coupling favorable agronomical traits (e.g. fruit quality, yield) with a higher resistance toward the mite.

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Porcine Post Weaning Diarrhoea (PWD) is one of the most important swine disease worldwide, caused by Enterotoxigenic Escherichia coli (ETEC) strains able to provoke management, welfare and sanitary issues. ETEC is determined by proteinaceous surface appendages. Numerous studies conducted by now in pigs have demonstrated, at the enterocytes level, that, the genes mucin 4 (MUC4) and fucosyltransferase (FUT1), coding for ETEC F4 and F18 receptors respectively, can be carriers of single nucleotide polymorphisms (SNPs) associated with natural resistance/susceptibility to PWD. The latter aspect was investigated in this study, evaluating the SNPs of the MUC4 and FUT1 genes in slaughtered pigs reared for the most in Central Italy. Genomic DNA was extracted from 362 swine diaphragmatic samples and then was subjected to the detection of known polymorphisms on MUC4 and FUT1candidate target genes by PCR-RFLP. Some of the identified SNPs were confirmed by sequencing analysis. Animals carrying the SNPs associated with resistance were 11% and 86% for the FUT1 and MUC4 genes respectively. Therefore, it can be assumed that the investigated animals may be an important resource and reservoir of favorable genetic traits for the breeding of pigs resistant to enterotoxigenic E.coli F4 variant.

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Osteogenesis is a complex multilevel process regulated by multiple genes. The GATA binding protein 4 (GATA4) gene has been extensively studied for its pivotal role in bone genesis and bone differentiation. However, its relationship with the growth traits of Shaanbei white cashmere (SBWC) and Guizhou black (GB) goats remains unclear. This work aims to investigate the potential influence of genetic mutations in the GATA4 gene on the growth traits goats. Thus, two Insertion/deletion (InDel) polymorphisms (8-bp-InDel and 9-bp-InDel) were screened and detected in a total of 1161 goats (including 980 SBWC goats and 181 GB goats) using PCR and agarose gel electrophoresis. The analyses revealed that there were two genotypes (ID and DD) for these two loci. In SBWC goats, 8-bp-InDel and 9-bp-InDel loci were significantly associated with heart girth (HG) and hip width (HW). Notably, individuals with DD genotype of 8-bp-InDel locus were superior while those with DD genotype of 9-bp-InDel locus were inferior. Correlation analyses of the four combined genotypes revealed significant associations with cannon circumference (CC), body height (BH), HG and HW. This work provides a foundation for the application of molecular marker-assisted selection (MAS) in goat breeding programs. Furthermore, the findings highlight the potential of the GATA4 gene and its genetic variations as valuable indicators for selecting goats with desirable growth traits.

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Fibroblast growth factor 7 (FGF7) is involved in lipid metabolism, which is considered as a candidate gene with close relation with muscle development by eGWAs and RNA-Seq analyses. To date, limited research has been conducted on the relationship between FGF7 gene and growth traits. The main objective of this work was to further investigate the association between novel InDel within FGF7 gene and growth traits in goat. Herein, FGF7 mRNA expression levels were investigated in various Fuqing goat tissues. We found that FGF7 gene was expressed in six adult goat tissues with the highest mRNA levels in adipose tissue. This result suggested that FGF7 gene might play a critical role in fat deposition. We also detected potential polymorphisms in Fuqing, Nubian and Jianyang Daer breeds. A 22-bp InDel polymorphism in FGF7 gene was detected in 396 goats and the three genotypes were designated as II, ID, and DD. Correlation analysis revealed that InDel polymorphism was significantly associated with growth traits (P < 0.05). Goats with genotypes ID and/or II had superior growth traits compared to those with genotype DD. In summary, our findings suggested that the 22-bp InDel within FGF7 gene could act as a molecular marker to improve the growth traits of goats in breeding programs.

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As a member of the SNX family, the goat sorting nexin 29 (SNX29) is initially identified as a myogenesis gene. Therefore, this study aimed to examine the polymorphism in the SNX29 gene and its association with growth traits. In this study, we used an online platform to predict the structures of the SNX29 protein and used quantitative real-time PCR to detect potential copy number variation (CNV) in Shaanbei white cashmere (SBWC) goats (n = 541), Guizhou black (GB) goats (n = 48), and Nubian (NB) goats (n = 39). The results showed that goat SNX29 protein belonged to non-secretory protein. Then, five CNVs were detected, and their association with growth traits was analyzed. In SBWC goats, CNV1, CNV3, CNV4, and CNV5 were associated with chest width and body length (P < 0.05). Among them, the CNV1 individuals with gain and loss genotypes were superior to those individuals with a median genotype, but CNV4 and CNV5 of individuals with the median genotype were superior to those with the loss and gain genotypes. In addition, individuals with the gain genotype had superior growth traits in CNV3. In brief, this study suggests that the CNV of SNX29 can be used as a molecular marker in goat breeding.

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The photoperiodic sensitivity of soybean (Glycine max L.) is one of the limiting factors affecting plant growth and yield. At higher latitudes, early flowering and maturity with neutral reaction to photoperiods are required for adaptation of soybean plants to long-day conditions. Currently, the production and distribution of new varieties of soybeans adapted to widespread agricultural regions in northern Kazakhstan is in strong demand. Eleven soybean hybrid populations were obtained from crosses between 17 parents with four maturity groups, MG 000, 00, 0, and I. Marker-assisted selection (MAS) was assessed for suitable SSR markers and successfully applied for genes E1, E3, E4, and E7, targeting homozygous genotypes with recessive alleles. The identified and selected genotypes were propagated and tested in the conditions of 53° N latitude in the Kostanay region of northern Kazakhstan. Finally, 20 early maturing F4 breeding lines were identified and developed with genotypes e1 e3 E4 e7, e1 E3 E4 e7, and e1 E3 e4 e7, all completing their growth period within 92-102 days. These breeding lines were developed by MAS and should provide very prospective superior varieties of soybean for northern Kazakhstan through a strategy that may be very helpful to other countries with high latitudes.

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A high-throughput genotyping platform with customized flexibility, high genotyping accuracy, and low cost is critical for marker-assisted selection and genetic mapping in soybean. Three assay panels were selected from the SoySNP50K, 40K, 20K, and 10K arrays, containing 41,541, 20,748, and 9670 SNP markers, respectively, for genotyping by target sequencing (GBTS). Fifteen representative accessions were used to assess the accuracy and consistency of the SNP alleles identified by the SNP panels and sequencing platform. The SNP alleles were 99.87% identical between technical replicates and 98.86% identical between the 40K SNP GBTS panel and 10× resequencing analysis. The GBTS method was also accurate in the sense that the genotypic dataset of the 15 representative accessions correctly revealed the pedigree of the accessions, and the biparental progeny datasets correctly constructed the linkage maps of the SNPs. The 10K panel was also used to genotype two parent-derived populations and analyze QTLs controlling 100-seed weight, resulting in the identification of the stable associated genetic locus Locus_OSW_06 on chromosome 06. The markers flanking the QTL explained 7.05% and 9.83% of the phenotypic variation, respectively. Compared with GBS and DNA chips, the 40K, 20K, and 10K panels reduced costs by 5.07% and 58.28%, 21.44% and 65.48%, and 35.74% and 71.76%, respectively. Low-cost genotyping panels could facilitate soybean germplasm assessment, genetic linkage map construction, QTL identification, and genomic selection. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01372-6.

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Soybean seed protein content (PC) and oil content (OC) have important economic value. Detecting the loci/gene related to PC and OC is important for the marker-assisted selection (MAS) breeding of soybean. To detect the stable and new loci for PC and OC, a total of 320 soybean accessions collected from the major soybean-growing countries were used to conduct a genome-wide association study (GWAS) by resequencing. The PC ranged from 37.8% to 46.5% with an average of 41.1% and the OC ranged from 16.7% to 22.6% with an average of 21.0%. In total, 23 and 29 loci were identified, explaining 3.4%-15.4% and 5.1%-16.3% of the phenotypic variations for PC and OC, respectively. Of these, eight and five loci for PC and OC, respectively, overlapped previously reported loci and the other 15 and 24 loci were newly identified. In addition, nine candidate genes were identified, which are known to be involved in protein and oil biosynthesis/metabolism, including lipid transport and metabolism, signal transduction, and plant development pathway. These results uncover the genetic basis of soybean protein and oil biosynthesis and could be used to accelerate the progress in enhancing soybean PC and OC.

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Background: The hippocampal abundant transcript 1 (HIAT1) gene, also known as major facilitator superfamily domain-containing 14A (MFSD14A), encodes for a transmembrane transporter protein and has been previously shown to be associated with milk production in buffalo and sheep breeds, as well as growth traits in chicken and goats. However, tissue level distribution of the ovine HIAT1 gene, as well as its effect on body morphometric traits in sheep, has yet to be studied. Methods: The HIAT1 mRNA expression profile of Lanzhou fat-tailed (LFT) sheep was determined by quantitative real-time PCR (qPCR). A total of 1498 sheep of three indigenous Chinese sheep breeds were PCR-genotyped for polymorphisms of HIAT1 gene. Student's t-test was used to observe the association between the genotype and sheep morphometric traits. Results: HIAT1 was widely expressed in all examined tissues, and was particularly abundant in the testis of male LFT sheep. Additionally, a 9-bp insertion mutation (rs1089950828) located within the 5'-upstream region of HIAT1 was investigated in Luxi black-headed (LXBH) sheep and Guiqian semi-fine wool (GSFW) sheep. The wildtype allele frequency 'D' was found to be more prevalent than that of the mutant allele 'I'. Furthermore, low genetic diversity was confirmed in all sampled sheep populations. Subsequent association analyses indicated an association between the 9-bp InDel mutation of interest and the morphometric traits of LXBH and GSFW sheep. Furthermore, yearling ewes with a heterozygous genotype (ID) demonstrated smaller body sizes, while yearling rams and adult ewes with the heterozygous genotype were found to have overall better growth performance. Conclusion: These findings imply that functional InDel polymorphism (rs1089950828) has the potential to be utilized for marker-assisted selection (MAS) of growth traits in domestic Chinese sheep populations.

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Breeding fruit species is time-consuming and expensive. With few exceptions, trees are likely the worst species to work with in terms of genetics and breeding. Most are characterized by large trees, long juvenile periods, and intensive agricultural practice, and environmental variability plays an important role in the heritability evaluations of every single important trait. Although vegetative propagation allows for the production of a significant number of clonal replicates for the evaluation of environmental effects and genotype × environment interactions, the spaces required for plant cultivation and the intensity of work necessary for phenotypic surveys slow down the work of researchers. Fruit breeders are very often interested in fruit traits: size, weight, sugar and acid content, ripening time, fruit storability, and post-harvest practices, among other traits relevant to each individual species. The translation of trait loci and whole-genome sequences into diagnostic genetic markers that are effective and affordable for use by breeders, who must choose genetically superior parents and subsequently choose genetically superior individuals among their progeny, is one of the most difficult tasks still facing tree fruit geneticists. The availability of updated sequencing techniques and powerful software tools offered the opportunity to mine tens of fruit genomes to find out sequence variants potentially useful as molecular markers. This review is devoted to analysing what has been the role of molecular markers in assisting breeders in selection processes, with an emphasis on the fruit traits of the most important fruit crops for which examples of trustworthy molecular markers have been developed, such as the MDo.chr9.4 marker for red skin colour in apples, the CCD4-based marker CPRFC1, and LG3_13.146 marker for flesh colour in peaches, papayas, and cherries, respectively.

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The Ug99-effective stem rust resistance gene Sr48 was mapped to chromosome 2A based on its repulsion linkage with Yr1 in an Arina/Forno recombinant inbred line (RIL) population. Attempts to identify markers closely linked to Sr48 using available genomic resources were futile. This study used an Arina/Cezanne F5:7 RIL population to identify markers closely linked with Sr48. Using the Arina/Cezanne DArTseq map, Sr48 was mapped on the short arm of chromosome 2D and it co-segregated with 12 markers. These DArTseq marker sequences were used for BlastN search to identify corresponding wheat chromosome survey sequence (CSS) contigs, and PCR-based markers were developed. Two simple sequence repeat (SSR) markers, sun590 and sun592, and two Kompetitive Allele-Specific PCR (KASP) markers were derived from the contig 2DS_5324961 that mapped distal to Sr48. Molecular cytogenetic analysis using sequential fluorescent in situ hybridization (FISH) and genomic in situ hybridization (GISH) identified a terminal translocation of chromosome 2A in chromosome 2DL of Forno. This translocation would have led to the formation of a quadrivalent involving chromosomes 2A and 2D in the Arina/Forno population, which would have exhibited pseudo-linkage between Sr48 and Yr1 in chromosome 2AL. Polymorphism of the closet marker sunKASP_239 among a set of 178 wheat genotypes suggested that this marker can be used for marker-assisted selection of Sr48.

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Streptococcus iniae is a problematic gram-positive bacterium negatively affecting Nile tilapia (Oreochromis niloticus), one of the main aquacultural species produced worldwide. The aim of this study was to identify the genetic architecture of survival to S. iniae and identify single nucleotide polymorphism (SNPs) linked to quantitative trait loci (QTL) related to survival to S. iniae challenge. With this purpose, Nile tilapia from the Spring Genetics breeding program were sent to a controlled S. iniae challenge test where phenotypes were scored as dead for fish that died during challenge test and survivors for the fish alive at the termination of the test. Additionally, fin-clip samples from all fish in the test were collected for DNA extraction. Out of 1904 fish in the challenge test, tissue samples of 321 fish were sent for genotyping using double digest restriction site associated DNA sequencing (ddRADseq). After quality control and filtering, 9,085 SNPs were used to perform a genome-wide association study (GWAS). A significant signal in LG8 was observed indicating association with survival to S. iniae challenge, with SNPs explaining from 12% to 26% of the genetic variance. To demonstrate the usefulness of marker assisted selection (MAS) to selectively breed fish for survival to S. iniae, offspring of breeding candidates classified as "resistant" and "susceptible" based on haplotypes of the four most significant markers were sent to a controlled S. iniae challenge test. At the end of the test, the differences in mortality between the two groups were strikingly different with a final cumulative percent mortality of less than 1% and 73% for offspring from "resistant" and "susceptible" parents, respectively. These results demonstrate that MAS for improved resistance to S. iniae is feasible.

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Leaf rust, caused by Puccinia triticina (Pt) is among the most devastating diseases posing a significant threat to global wheat production. The continuously evolving virulent Pt races in North America calls for exploring new sources of leaf rust resistance. A diversity panel of 365 bread wheat accessions selected from a worldwide population of landraces and cultivars was evaluated at the seedling stage against four Pt races (TDBJQ, TBBGS, MNPSD and, TNBJS). A wide distribution of seedling responses against the four Pt races was observed. Majority of the genotypes displayed a susceptible response with only 28 (9.8%), 59 (13.5%), 45 (12.5%), and 29 (8.1%) wheat accessions exhibiting a highly resistant response to TDBJQ, TBBGS, MNPSD and, TNBJS, respectively. Further, we conducted a high-resolution multi-locus genome-wide association study (GWAS) using a set of 302,524 high-quality single nucleotide polymorphisms (SNPs). The GWAS analysis identified 27 marker-trait associations (MTAs) for leaf rust resistance on different wheat chromosomes of which 20 MTAs were found in the vicinity of known Lr genes, MTAs, or quantitative traits loci (QTLs) identified in previous studies. The remaining seven significant MTAs identified represent genomic regions that harbor potentially novel genes for leaf rust resistance. Furthermore, the candidate gene analysis for the significant MTAs identified various genes of interest that may be involved in disease resistance. The identified resistant lines and SNPs linked to the QTLs in this study will serve as valuable resources in wheat rust resistance breeding programs.

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The Homeobox A11 (HOXA11) gene regulates limb skeletal development and muscle growth, thus, it was selected as a candidate gene for bovine carcass traits. In this study, we analyzed the mRNA expression level of HOXA11 in various tissues and cells, and determined the genetic variations in the HOXA11 gene, which might be used as molecular markers for cattle breeding. The mRNA expression profiles of HOXA11 in bovine different tissues showed that HOXA11 was highly expressed in both fat and muscle. The gene expression trend of HOXA11 in myoblasts and adipocytes indicated that HOXA11 might be involved in the differentiation of bovine myoblasts and adipocytes. The data in the Ensembl database showed that there are two putative insertion/deletion (InDel) polymorphisms in the bovine HOXA11 gene. The insertion site (rs515880802) was located in the upstream region (NC_037331.1: g. 68853364-68853365) and named as P1-Ins-4-bp, and the deletion site (rs517582703) was located in the intronic region (NC_037331.1: g. 68859510-68859517) and named as P2-Del-8-bp. These polymorphisms within the HOXA11 gene were identified and genotyped by PCR amplification, agarose gel electrophoresis and DNA sequencing in the 640 Shandong Black Cattle Genetic Resource (SDBCGR) population. Moreover, the mutation frequency was very low after detection, so the mathematical expectation (ME) method was used for detection. Statistical analysis demonstrated that P1-Ins-4-bp was significantly correlated with the beef shoulder (p = 0.012) and tongue root (p = 0.004). Meanwhile, P2-Del-8-bp displayed a significant correlation with the back tendon (p = 0.008), money tendon (p = 2.84 × 10-4), thick flank (p = 0.034), beef shin (p = 9.09 × 10-7), triangle thick flank (p = 0.04), triangle flank (p = 1.00 × 10-6), rump (p = 0.018) and small tenderloin (p = 0.043) in the female SDBCGR population. In summary, these outcomes may provide a new perspective for accelerating the molecular breeding of cattle through marker-assisted selection (MAS) strategies.

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Bean leaf crumple virus (BLCrV) is a novel begomovirus (family Geminiviridae, genus Begomovirus) infecting common bean (Phaseolus vulgaris L.), threatening bean production in Latin America. Genetic resistance is required to ensure yield stability and reduce the use of insecticides, yet the available resistance sources are limited. In this study, three common bean populations containing a total of 558 genotypes were evaluated in different yield and BLCrV resistance trials under natural infection in the field. A genome-wide association study identified the locus BLC7.1 on chromosome Pv07 at 3.31 Mbp, explaining 8 to 16% of the phenotypic variation for BLCrV resistance. In comparison, whole-genome regression models explained 51 to 78% of the variation and identified the same region on Pv07 to confer resistance. The most significantly associated markers were located within the gene model Phvul.007G040400, which encodes a leucine-rich repeat receptor-like kinase subfamily III member and is likely to be involved in the innate immune response against the virus. The allelic diversity within this gene revealed five different haplotype groups, one of which was significantly associated with BLCrV resistance. As the same genome region was previously reported to be associated with resistance against other geminiviruses affecting common bean, our study highlights the role of previous breeding efforts for virus resistance in the accumulation of positive alleles against newly emerging viruses. In addition, we provide novel diagnostic single-nucleotide polymorphism markers for marker-assisted selection to exploit BLC7.1 for breeding against geminivirus diseases in one of the most important food crops worldwide.

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BACKGROUND: During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype. RESULTS: A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker. CONCLUSIONS: The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.

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