Genetic Analysis Research Articles

MicroRNA399s and strigolactones mediate systemic phosphate signaling between dodder‐connected host plants and control association of host plants with rhizosphere microbes

Summary A dodder (Cuscuta) often simultaneously parasitizes two or more adjacent hosts. Phosphate (Pi) deficiency is a common stress for plants, and plants often interact with soil microbes, including arbuscular mycorrhizal fungi (AMF), to cope with Pi stress. Little is known about whether dodder transmits Pi deficiency‐induced systemic signals between different hosts. In this study, dodder‐connected plant clusters, each composed of two tobacco (Nicotiana tabacum) plants connected by a dodder, were established, and in each cluster, one of the two tobacco plants was treated with Pi starvation. AMF colonization efficiency, rhizosphere bacterial community, and transcriptome were analyzed in the other dodder‐connected Pi‐replete tobacco plant to study the functions of interplant Pi signals. We found that dodder transfers Pi starvation‐induced systemic signals between host plants, resulting in enhanced AMF colonization, changes of rhizosphere bacterial communities, and alteration of transcriptomes in the roots of Pi‐replete plants. Importantly, genetic analyses indicated that microRNA399s (miR399s) and strigolactones suppress the systemic Pi signals and negatively affect AMF colonization in the Pi‐replete plants. These findings provide new insight into the ecological role of dodder in mediating host–host and host–microbe interactions and highlight the importance of strigolactone and miR399 pathways in systemic Pi signaling.

Maternal Genetic Diversity Analysis of Guanling Cattle by Mitochondrial Genome Sequencing

Maternal Genetic Diversity Analysis of Guanling Cattle by Mitochondrial Genome Sequencing

Identification of heterozygous mutations of ABCC8 gene responsible for maturity-onset diabetes of the young with exome sequencing

Abstract Background Although the MODY12 subtype, caused by ABCC8 mutations, is rare, it is highly sensitive to sulfonylureas. The identification of ABCC8 mutations in patients clinically diagnosed with MODY has the ability to contribute to the precise management of diabetes. Methods Genetic analysis of two families with MODY were conducted using whole-exome sequencing (WES) and Sanger sequencing. The spatial structures of the mutant proteins were constructed using MODELLER and PyMOL software to provide further evidence of pathogenicity. Results The heterozygous missense mutations V357I and R1393H in ABCC8 were found in probands of two unrelated MODY pedigrees, which co-segregated with the hyperglycemic phenotypes in these two pedigrees. Detection of the V357I mutation enabled the proband of family A to successfully transfer from insulin to sulfonylurea (SU). After 3 months of follow-up for the SU trial, the HbA1c level of proband A improved from 12.4% at the initial diagnosis to 7.20%. Proband B was treated with insulin because of pregnancy and poor islet function. In silico analysis indicated that the R1393H mutation resulted in a longer hydrogen bond distance to L1389 and cleavage of carbon-hydrogen bonds to V1395, A1390, and L1389. Conclusions We have described two pathogenic missense mutations in ABCC8 in Chinese families with MODY. Our findings support the heterogeneity in the clinical features of MODY12 caused by ABCC8 mutations.

Exploring the Molecular Interaction Between NR2E3 and NR1D1 in Retinitis Pigmentosa: A Docking and Molecular Dynamics Study

ABSTRACTBackground and AimsRetinitis pigmentosa (RP) is a hereditary retinal disorder that gradually leads to vision loss due to photoreceptor cell degeneration. This study aims to investigate the clinical features and genetic underpinnings of RP within a large Iranian family. Our focus centered on mutations in the NR2E3 gene, which plays a critical role in the development and maintenance of the retina.MethodsTwenty‐five family members showed symptoms of RP, and fourteen of them underwent clinical examinations conducted by geneticists and ophthalmologists. The DNA samples of five individuals diagnosed with RP from the family were subjected to whole‐exome sequencing (WES) as part of the study. The candidate variant identified through WES was subsequently confirmed using bidirectional sequencing in additional family members. Additionally, in silico analysis, including molecular modeling, protein–protein docking, and molecular dynamics simulation (MD), was employed to assess potential pathogenic effects associated with the candidate variants.ResultsOphthalmic examination revealed night blindness, which is a common symptom among affected individuals. Genetic analysis identified a homozygous missense variant (c.934G>A/p.R311Q) in NR2E3 exon 6, which co‐segregates with other affected family members. Furthermore, molecular docking analysis indicated potential disruption in the binding affinity between NR2E3 and NR1D1 proteins. In‐depth, molecular dynamics analysis, considering parameters such as RMSD, RMSF, and hydrogen bonding, revealed notable differences between normal and mutant protein complexes.ConclusionExploring the molecular interaction between NR2E3 and NR1D1 provides new insights into the pathogenic mechanism of the p.R311Q mutation in RP.

Testing germination of common milkweed (Asclepias syriaca) from different study sites in the Niagara Region

Prior to 2014, the milkweed (Asclepias spp.) was listed as a noxious weed, contributing to its population’s decline in Canada. Considering its importance for the lifecycle of the threatened monarch butterfly (Danaus plexippus), it has been de-listed, and efforts are in place to re-establish the populations. Seed propagation may assist in increasing the population, but germination is difficult. The objectives of this study were to 1) test the efficacy of three different germination protocols: cold stratification, mechanical scarification, and chemical treatment of ascorbic acid and 2) determine whether environmental conditions could potentially influence germination. Independent experiments were conducted in petri dishes and in soil, from seeds collected from three sites. In both experiments, mechanical scarification was the most effective pre-germination treatment, followed by cold stratification (4℃). Germination rates differed among sites with site 3 having the largest germination rate. The tallest seedlings with the largest number of leaves (height mean=5.95, p<0.05) were from site 2. Variability might be the result of maternal and environmental effects as plants were exposed to different light intensity and disturbance intensity. Future research should consider conducting genetic analysis on the influence of maternal environmental effects on seed germinability to improve propagation.

Generation of viable hypomorphic and null mutant plants via CRISPR-Cas9 targeting mRNA splicing sites.

Genetic analysis is important for modern plant molecular biology, and in this regard, the existence of specific mutants is crucial. While genome editing technologies, particularly CRISPR-Cas9, have revolutionized plant molecular biology by enabling precise gene disruption, knockout methods are ineffective for lethal genes, necessitating alternatives like gene knockdown. This study demonstrates the practical generation of a hypomorphic mutant allele, alongside severe null mutant alleles, via the targeting of mRNA splicing sites using CRISPR-Cas9. The Arabidopsis HIGH PLOIDY 2 (HPY2) encodes a yeast NSE2 ortholog, part of the conserved eukaryotic SMC5/6 complex, with SUMO E3 ligase activity essential for cell cycle progression and plant development. Loss-of-function HPY2 mutants exhibit severe dwarfism and seedling lethality, making functional analysis challenging. To overcome these limitations, we created HPY2 knockdown mutants as novel tools to investigate gene function. Of the three mutant alleles, the hpy2-cr1 and hpy2-cr2 mutants resembled the existing severe hpy2-1 allele, both harboring a single base pair insertion in one exon, causing significant root shortening and seedling lethality. In contrast, the hypomorphic mutant hpy2-cr3, which has a five bp deletion at an intron-exon junction, showed relatively longer root growth and survived until the reproductive stage. RT-PCR analysis of hpy2-cr3 revealed atypical mRNAs producing truncated polypeptides that retained some HPY2 function, explaining the milder phenotype. These results establish the successful generation of novel hypomorphic mutant alleles critical for studying the lethal gene HPY2, and demonstrate the usefulness of CRISPR-Cas9 for producing viable hypomorphic mutants for investigating complex genetic interactions.

Assessment of Terminal Heat Stress Tolerance in Doubled Haploids Derived from Synthetic Hexaploid Wheat (Triticum aestivum L.) Using Genetic Variability and PCA-based Cluster Analyses

A comprehensive study was conducted on germplasm derived from two synthetic wheats and two hexaploid wheats i.e., SHW14102 x BWL4444, SHW14102 x BWL3531, and SHW3761 x BWL4444 to identify the potential doubled haploids that can withstand high temperatures, particularly at the reproductive stage during crop seasons viz., 2020–2021 and 2021–2022. The doubled haploid lines were selected based on phenotypic characteristics using genetic variability analysis. In the preliminary field trial evaluation, 100 lines were selected based on high phenotypic uniformity for further testing against terminal heat stress conditions and high yield potential. Among these, 17 lines had relatively higher values for days to biomass yield, grain yield, thousand-grain weight, and harvest index and relatively lower values for maturity, and grain filling duration based on principal component and cluster analyses. Principal component analysis (PCA) based cluster analysis exhibited that, clusters II and III had clear separation compared to cluster I. All three clusters were analyzed according to their means and standard deviations. The mean values for GYP (385.07), BMYP (1162.37), and TGW (38.13) were relatively higher in cluster 1 than in other clusters. Cluster 2 exhibited a higher value for DH (89.14), SL with awns (18.21), and GFD (18.19) while cluster 3 showed a higher value for HI (41.02). Thus, it was concluded that cluster I demonstrated superior performance in grain yield per plant, biomass yield per plant, and thousand-grain weight, indicating its overall higher productivity compared to the other clusters under terminal heat stress conditions and suggesting them as potential germplasm for future breeding programs.

Genetic, Clinical, and Biochemical Characterization ofa Large Cohort of Palestinian Patients With Fanconi-Bickel Syndrome.

This study aims to investigate the clinical, biochemical, and genetic characteristics of Fanconi-Bickel syndrome (FBS) in a cohort of 20 individuals from Palestine and to identify novel pathogenic variants. A retrospective analysis was conducted on medical records from Al-Makassed Hospital's pediatric department spanning 2015 to 2023. Individuals diagnosed with FBS via molecular genetic testing were included in the study. Among the 20 genetically confirmed FBS patients, hepatomegaly was prevalent in 95%, whereas 70% exhibited both developmental delay and hypophosphatemic rickets, and 68.4% experienced growth retardation. Hypertriglyceridemia (HTG) was universal. Elevated liver enzymes and alkaline phosphatase were common, along with hypophosphatemia (95%) and urinary abnormalities. Genetic analysis revealed five distinct SLC2A2 pathogenic variants, including three previously unreported variants: p.Gln23Arg (c.68A > G), p.Thr353Arg (c.1058_1059delinsGG), and an exon 7 deletion. This study presents the largest single-center cohort of FBS patients, expanding our understanding of the disorder's phenotypic and genotypic spectrum. Despite FBS generally carrying a favorable prognosis, timely diagnosis remains crucial to prevent severe complications.

Global Invasion of Thrips parvispinus (Karny) (Thysanoptera: Thripidae) Across Three Continents Associated With Its One Haplotype

ABSTRACTThrips parvispinus (Karny) is an exotic pest that has invaded many regions around the world in the last three decades. It was first detected in Florida in 2020 on ornamental plants (Hoya and Anthurium) in greenhouses and subsequently on ornamental plants in residential landscapes (Gardenia) in 2021. However, its first report on open vegetable field crops (Capsicum) in Florida was in 2022. We conducted field surveys and genetic analysis to answer three questions: (1) Is the population of T. parvispinus that invaded Florida the same as the one that has spread globally in the last few decades? (2) Is the host expansion to Capsicum in Florida a new population or the extension of the existing population reported on ornamental plants? and (3) What are the native and invaded distribution ranges of T. parvispinus? We analysed the genetic variation in the mitochondrial gene cytochrome oxidase I (COI) to address these questions. The global genetic diversity analysis of T. parvispinus revealed 18 haplotypes (populations) worldwide based on available data, but only one population (Hap1) invaded three continents: Africa, Europe, and North America. Based on available data, the highest haplotype diversity was observed in India, suggesting India may be part of the presumed native range (South and Southeast Asian countries) of T. parvispinus. Our survey of retail plant stores across 10 Florida counties indicated that plant trade is the source of T. parvispinus in open vegetable field crops and ornamental landscape plants. The outcome of this study will assist with regulatory and management decisions of T. parvispinus in Florida and elsewhere.

OsIAA23 Promotes Heading by Directly Downregulating Ghd7 in rice.

Ghd7 is a central regulator to multiple growth and development processes in rice. While it is not clear how Ghd7 is regulated by upstream factors. To identify its upstream regulator, the truncated Ghd7 promoter fragments were used to screen cis elements binding to rice total nuclear proteins. Electrophoretic mobility shift assays screened one truncated fragment f3 binding to the proteins. Subsequently, the fragment f3 was employed to screen a yeast one-hybrid library, and a transcription factor OsIAA23 was screened as a direct upstream regulator of Ghd7. Dual-luciferase transient assay demonstrated the transcriptional repression effect of OsIAA23 on the activity of Ghd7, and the location of the cis elements binding to OsIAA23 in the region 1264 to 1255bp upstream of ATG. Genetic analysis between the wild type Ghd7-OsIAA23 and single/double mutants further verified that OsIAA23 downregulated Ghd7 expression and led to a delayed heading under long day conditions. Moreover, natural variations in fragment f3 were associated with heading and geographic distribution in rice. This study sheds light on the direct regulatory mechanism of OsIAA23 on Ghd7, which enriches the understanding of the Ghd7 involved flowering regulatory network in rice.

Expanding diversity within phenylketonuria in ecuadorian patients: genetic analysis and literature review of newborn screenings.

Phenylketonuria (PKU) is an autosomal recessive metabolic disorder caused by a deficiency in the phenylalanine hydroxylase (PAH) enzyme, leading to the accumulation of phenylalanine and its metabolites, which are toxic to the central nervous system. Without treatment, PKU can result in severe intellectual disability and neurological issues. This study aims to present the first cohort of clinically described Ecuadorian PKU patients, analyzing genotype-phenotype correlations and comparing these variants with global databases to improve diagnosis and treatment in Ecuador. Detailed clinical histories were collected, and an analysis of genotype versus phenotype (affected protein domain) of the variant was performed. Among the PAH genotypes identified, we found 15 distinct variants, with c.[754C > T](p.Arg252Trp); [754C > T](p.Arg252Trp) being the most frequent genotype (23.68%), followed by c.[1045T > C](p.Ser349Pro); [1045T > C](p.Ser349Pro) (15.79%) and c.[441 + 5G > T]; [754C > T](p.Arg252Trp) (13.16%). Additionally, several unique genotypes were identified, such as c.[140G > A](p.Ala47Val); [140G > A](p.Ala47Val) and c.[331C > T](p.Arg111Ter); [1243G > A](p.Asp415Asn), which are not commonly reported in other populations. Most genotypes were heterozygous (63.2%). The majority of variants were missense variants (66.6%) affecting the catalytic domain (53.3%). The highest phenylalanine levels were found in patients with c.[754C > T](p.Arg252Trp); [754C > T] (p.Arg252Trp) (2700 umol/L). Phenotypic data were available for 11 patients, showing 45.45% with classic PKU, 45.45% with mild hyperphenylalaninemia, and 9% with mild PKU. There was a 63.6% concordance with the BIOPKU database. Five low-frequency genotypes not reported in BIOPKU were identified, suggesting unique regional variants. Our study highlights the genetic complexity of PKU in Ecuador, with a high prevalence of unique variants not commonly found in other regions. This underscores the necessity for region-specific genetic analysis to improve PKU diagnosis and treatment. The findings emphasize the importance of tailored therapeutic strategies and continued research to enhance outcomes for PKU patients in Latin America.

Population structure and selective signature analysis of local sheep breeds in Xinjiang, China based on high-density SNP chip.

The frigid and droughty climate of Xinjiang in China has given rise to unique indigenous sheep breeds with robust adaptability and resistance. To investigate the genetic mechanism of adaptability of Xinjiang sheep to the local extreme environment, we conducted population genetic structure analyses for three native Xinjiang sheep breeds: Altay sheep (ALT), Bashbay Sheep (BSBC), and Duolang sheep (DLC), as well as two foreign sheep breeds: Suffolk and Dorset, using the Ovine Infinium HD SNP BeadChip(680K). Our findings revealed distinct genetic and evolutionary histories between Xinjiang and foreign sheep breeds. Principal Component Analysis (PCA) and phylogenetic tree effectively differentiate these five sheep breeds based on their geographical origins, and the domestication level of Xinjiang sheep is comparatively lower than that of foreign sheep breeds. Furthermore, by utilizing three selective signature methods, namely Fixation Index (Fst), Cross Population Extended Haplotype Homozygosity Test (XP-EHH), and Nucleotide Diversity (π), we have successfully identified 22 potential candidate genes. Among these genes, there are TBXT, PDGFD, and VEGFA, which are closely related to tail type and lipid metabolism; VIL1, SLC11A1, and ZBTB46, which are associated with immune function; and candidate genes such as BNC1, HDAC1, and BMP5, which impact sheep reproductive traits. This study establishes a foundation for conserving and utilizing local sheep germplasm resources in Xinjiang and provides molecular insights into the genetic mechanisms governing sheep adaptation to extreme cold and arid environments.

Gender-modulated influence of BDNF concentration and Val66Met polymorphism on cognitive outcomes in chronic limb ischemia patients

IntroductionWhile numerous studies have established associations between brain-derived neurotrophic factor (BDNF) and cognitive functioning, limited research has delved into the role of BDNF concerning cognitive outcomes in atherosclerosis-related conditions. This study aimed to investigate the correlations between cognitive performance, serum BDNF levels, and the BDNF Val66Met polymorphism in individuals diagnosed with chronic limb ischemia (CLI).Participants and procedureThe study encompassed 159 CLI patients (52 females, 107 males) aged 59-73 years. Genetic analysis involved assessing the BDNF Val66Met single-nucleotide polymorphism using a TaqMan SNP Genotyping Assay and the ViiA™ 7 Real-Time PCR System. Serum BDNF levels were quantified. Cognitive functioning was evaluated through a computerized battery of tests, including the simple reaction test (SRT) for speed and accuracy assessment, verbal memory test (VMT) for short and long-term memory evaluation, and the GoNoGo test for cognitive control and inhibition.ResultsGender differences in cognitive performance were observed, with women excelling in VMT, while men demonstrated superior performance in SRT and the GoNoGo test. No statistically significant differences were noted between the Met/Met or Met/Val and Val/Val subgroups. However, notable differences emerged in female Met carriers, exhibiting superior VMT scores but more incorrect Go responses in the GoNoGo test. Conversely, female Val homozygotes showed significantly more incorrect NoGo responses compared to male Val homozygotes. In men carrying the Met allele, higher BDNF concentrations correlated with improved GoNoGo test results (r = 0.248, p = 0.01). Conversely, in women with the Val/Val variant, lower BDNF concentrations were associated with better VMT scores.ConclusionsThis study underscores the sex-specific impact of BDNF serum levels and the BDNF polymorphism on cognitive processes among CLI patients. The findings highlight the nuanced influence of BDNF in shaping cognitive functioning, emphasizing the need for further research into these sex-dependent associations.

Genetic connectivity of wolverines in western North America.

Wolverine distribution contracted along the southern periphery of its range in North America during the 19th and 20th centuries due primarily to human influences. This history, along with low densities, sensitivity to climate change, and concerns about connectivity among fragmented habitats spurred the recent US federal listing of threatened status and special concern status in Canada. To help inform large scale landscape connectivity, we collected 882 genetic samples genotyped at 19 microsatellite loci. We employed multiple statistical models to assess the landscape factors (terrain complexity, human disturbance, forest configuration, and climate) associated with wolverine genetic connectivity across 2.2million km2of southwestern Canada and the northwestern contiguous United States. Genetic similarity (positive spatial autocorrelation) of wolverines was detected up to 555km and a high-to-low gradient of genetic diversity occurred from north-to-south. Landscape genetics analyses confirmed that wolverine genetic connectivity has been negatively influenced by human disturbance at broad scales and positively influenced by forest cover and snow persistence at fine- and broad-scales, respectively. This information applied across large landscapes can be used to guide management actions with the goal of maintaining or restoring population connectivity.

Drug-resistant BRAF V600E-mutant recurrent pleomorphic xanthoastrocytoma, CNS WHO Grade 3 successfully resolved with incidental discontinuation of combined BRAF and MEK inhibitor therapy

Background: Combination therapy with BRAF and MEK inhibitor holds promise for treating gliomas harboring the BRAF V600E mutation; however, the development of acquired resistance remains a challenge. Case Description: We describe a case of repeated recurrent BRAF-mutant pleomorphic xanthoastrocytoma (central nervous system World Health Organization grade 3) treated with combination therapy with BRAF and MEK inhibitor. The patient received dabrafenib (BRAF inhibitor) and trametinib (MEK inhibitor); however, she developed resistance to the combination therapy. Remarkably, incidental drug discontinuation contributed to the disappearance of the resistant tumor. The same phenomenon was repeatedly observed after that. Genetic analysis demonstrated that the resistant tumor had BRAF V600E amplification; the resistant tumor remained BRAF→MEK→ERK pathway dependent, and drug resistance might be due to elevated BRAF V600E expression. We speculated that ERK1/2 signal extremes caused by the discontinuation of the combination therapy affected the resistant tumor survival. Conclusion: This case study provides important insights into novel treatment strategies and their underlying mechanisms for gliomas with BRAF mutations.

Plasmodium falciparum genetic diversity and multiplicity of infection among asymptomatic and symptomatic malaria-infected individuals in Uganda.

Plasmodium falciparum (P. falciparum) remains a significant public health challenge globally, especially in sub-Saharan Africa (SSA), where it accounts for 99% of all malaria infections. The outcomes of P. falciparum infection vary, ranging from asymptomatic to severe, and are associated with factors such as host immunity, parasite genetic diversity, and multiplicity of infection (MOI). Using seven neutral microsatellite markers, the current study investigated P. falciparum genetic diversity and MOI in both asymptomatic and symptomatic malaria individuals in Uganda. This cross-sectional study analyzed 225 P. falciparum isolates from both asymptomatic and symptomatic malaria patients, ranging in age from 6months to ≥ 18years. P. falciparum genetic diversity, MOI, and multi-locus linkage disequilibrium (LD) were assessed through genotyping of seven neutral microsatellite markers: Poly-α, TA1, TA109, PfPK2, 2490, C2M34-313, and C3M69-383. Genetic data analysis was performed using appropriate genetic analysis software. P. falciparum infections exhibited high genetic diversity in both asymptomatic and symptomatic individuals. The mean expected heterozygosity (He) ranged from 0.79 in symptomatic uncomplicated malaria cases to 0.81 in asymptomatic individuals. There was no significant difference (p = 0.33) in MOI between individuals with asymptomatic and symptomatic infections, with the mean MOI ranging from 1.92 in symptomatic complicated cases to 2.10 in asymptomatic individuals. Polyclonal infections were prevalent, varying from 58.5% in symptomatic complicated malaria to 63% in symptomatic uncomplicated malaria cases. A significant linkage disequilibrium (LD) was observed between asymptomatic and symptomatic uncomplicated/complicated infections (p < 0.01). Genetic differentiation was low, with FST values ranging from 0.0034 to 0.0105 among P. falciparum parasite populations in asymptomatic and symptomatic uncomplicated/complicated infections. There is a high level of P. falciparum genetic diversity and MOI among both symptomatic and asymptomatic individuals in Uganda. Asymptomatic carriers harbor a diverse range of parasites, which poses challenges for malaria control and necessitates targeted interventions to develop effective strategies.

Novel sequence types and low levels of antimicrobial resistance associated with clinical mastitis in sheep flocks across Scotland.

This research paper aimed to demonstrate that mammary secretions provided by sheep farmers across Scotland from cases of clinical mastitis are free from environmental contamination, as well as to provide information on the major bacterial causes of disease and levels of antimicrobial resistance. Mastitis represents one of most significant diseases of small ruminant production worldwide. Staphylococcus aureus, Mannheimia haemolytica, Streptococcus uberis and coagulase-negative Staphylococcal species are common pathogens isolated from cases of sheep mastitis. Sampling kits supplied to 23 farms provided 33 samples for bacteriology, antimicrobial susceptibility testing and genetic analysis. Of the bacterial isolates identified, 60% were S. aureus, 23% M. haemolytica and 7% coagulase-negative staphylococci. Low levels of antimicrobial resistance were identified in the S. aureus isolates which provided novel multi-locus sequence types. In conclusion, this proof-of-concept survey demonstrated that mammary secretions free from environmental contamination may be provided by sheep farmers. It also provided data on the prevalence of antimicrobial resistance associated with clinical mastitis in sheep and will inform on the scale required for larger surveys aiming to improve current strategies for mastitis control in sheep flocks across the UK.

Identification and Gene Fine Mapping of the Bisexual Sterility Mutant Meiosis Abnormal Bisexual Sterility 1 in Rice

Exploring the genes regulating rice fertility is of great value for studying the molecular mechanisms of rice reproductive development and production practices. In this study, we identified a sterile mutant from the mutant library induced by ethyl methanesulfonate (EMS), designated as meiosis abnormal bisexual sterility 1 (mabs1). The mabs1 mutant exhibits no phenotypic differences from the wild-type during the vegetative growth phase but shows complete sterility during the reproductive growth phase. Phenotypic observations revealed that both pollen and embryo sac fertility are lost in mabs1. Notably, in mabs1, the development of the anther inner and outer walls, tapetum degeneration, and callose synthesis and degradation all proceed normally, yet meiosis fails to form normal tetrads. Genetic analysis indicated that this mutant trait is controlled by a single recessive nuclear gene. By constructing a genetic segregation population, we successfully mapped the MABS1 gene to a 49 kb region between primer markers Y7 and Y9 on chromosome 1. Resequencing revealed a single-nucleotide substitution in the exon of the LOC_Os01g66170 gene, which resulted in a change from Valine to Isoleucine. Subsequent sequencing of this locus in both wild-type and mabs1 mutants confirmed this mutation. Therefore, we have identified the gene at LOC_Os01g66170 as a candidate for MABS1, a previously unreported novel gene involved in rice meiosis. Through RT-qPCR, we found that the expression levels of multiple meiosis-related genes were significantly changed in the mabs1 mutant. Therefore, we believe that MABS1 is also involved in the process of rice meiosis. This study lays the groundwork for a functional study of MABS1.

Pre-breeding highlights of intraspecific polymorphism and genetic estimates of seed traits of African yam bean (Sphenostylis stenocarpa Hochst Ex. A. Rich.) Harms breeding lines

Abstract Discriminatory morpho-metric features are obvious on legume seeds. This study utilized seven quantitative and 11 qualitative seed traits to characterize 139 African yam bean (AYB) breeding lines which were developed through single seed descent procedure. The seven quantitative data were subjected to analysis of variance, their means were combined with qualitative scores for genetic distance, principal component (PC) and clustering analyses. Significant (P ≤ 0.001) variation existed among the breeding lines for the seven traits. Mean ranges of seed length (SL), width (SW), thickness (ST) and a single seed weight (SSW) among the 139 breeding lines were respectively: 6.77–10.22 mm, 5.70–7.86 mm, 4.96–7.45 mm and 0.15–0.42 g. Positive and significant (P ≤ 0.05) genotypic correlation existed among SSW, SL, SW and ST. Seed colours, pattern, shapes, sizes, surface texture, brilliance varied among the breeding lines. Ranges of phenotypic and genotypic coefficient of variation and broadsense heritability were: 5.49–23.84%, 2.95–19.88% and 28.91–69.54% respectively. Fourteen (quantitative and qualitative) traits contributed higher (≥ 0.30) eigenvector loadings to the first three PC axes which explained 57.9% of the total variation among the breeding lines. Similarity among the lines was 0.75. Four clusters ensued in the dendrograph and each group had genetic similarities of: 0.85 (I), 0.82 (II), 0.78 (III) and 0.80 (IV). This research unveiled significant variation among AYB breeding lines with promising reliability for breeding opportunities of the qualitative and quantitative seed traits, which could contribute to higher grain yield and acceptability.

Quantitative trait locus mapping and OsFLOq12 identification for rice grain hardness: towards improved rice flour for wheat substitution.

Recent shifts in consumer dietary preferences have led to a significant decline in rice consumption in Korea, resulting in surplus rice production. To address this issue, rice flour has been proposed as a substitute for wheat flour. However, the physical, chemical and structural differences between rice and wheat, particularly in grain hardness, pose challenges in using rice flour as an alternative. Understanding the genetic factors that influence rice grain hardness is crucial for improving the milling process and producing high-quality rice flour suitable for wheat flour substitution. In this study, various grain traits, including length, width, thickness, length-to-width ratio and hardness, were measured in a population of brown and milled rice. Quantitative trait locus (QTL) analysis revealed a significant association between grain hardness and thickness, with QTLs for grain hardness mapped on chromosomes 1 and 12 for brown and milled rice, respectively. A total of 20 candidate genes related to grain hardness were identified through QTL analysis. Among them, OsFLOq12 (LOC_Os12g43550) was identified as a key gene influencing grain hardness, which encodes a Ras small GTPase. Phenotypic analysis showed differences in endosperm appearance and particle size between lines with low and high grain hardness. The genetic analysis of OsFLOq12 revealed a single nucleotide polymorphism associated with grain hardness. This study provides valuable insights into the genetic background of grain hardness, offering a foundation for breeding rice varieties optimized for flour production as a viable substitute for wheat flour. © 2024 Society of Chemical Industry.