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Cowpea [Vigna unguiculata (L.) Walp.] is an important grain legume which is widely grown in Sub-Saharan Africa (SSA) for food and feed. Its grain contains high levels of protein, energy, micro- and macro-nutrients. In SSA cowpea productivity is considerably low due to a wide array of abiotic and biotic stresses, and socio-economic constraints. This review summarizes challenges and constraints to cowpea production, breeding methods and progress, genetic variation and analysis of cowpea. Therefore, this review could serve as baseline information for cowpea breeders, agronomists and producers in Namibia as well as for similar agro-ecologies in SSA.

Background: Genetic improvement for Striga hermonthica (Sh) and S. asiatica (Sa) resistance is the most economical and effective control method to enhance the productivity of maize and other major cereal crops. Hence, identification of quantitative trait loci (QTL) associated with Striga resistance and economic traits will guide the pace and precision of resistance breeding in maize. The objective of this study was to undertake a genome-wide association analysis of grain yield and Sh and Sa resistance among tropical and sub-tropical maize populations to identify putative genetic markers and genes for resistance breeding. 126 maize genotypes were evaluated under controlled environment conditions using artificial infestation of Sh and Sa. The test genotypes were profiled for grain yield (GY), Striga emergence counts at 8 (SEC8) and 10 (SEC10) weeks after planting, and Striga damage rate scores at 8 (SDR8) and 10 (SDR10) weeks after planting. Population structure analysis and genome-wide association mapping were undertaken based on 16,000 single nucleotide polymorphism (SNP) markers., Results: A linkage disequilibrium (LD) analysis in 798,675 marker pairs revealed that 21.52% of pairs were in significant linkage (P < 0.001). Across the chromosomes, the LD between SNPs decayed below a critical level (r 2  = 0.1) at a map distance of 0.19 Mbp. The genome-wide association study identified 50 significant loci associated with Sh resistance and 22 significant loci linked to Sa resistance, corresponding to 39 and 19 candidate genes, respectively., Conclusion: The study found non-significant QTL associated with dual resistance to the two examined Striga species Some of the detected genes reportedly conditioned insect and pathogen resistance, plant cell development, variable senescence, and pollen fertility. The markers detected in the present study for Sa resistance were reported for the first time. The gene Zm00001eb219710 was pleiotropic, and conditioned GY and SEC10, while Zm00001eb165170 affected SDR8 and SDR10, and Zm00001eb112030 conditioned SDR8 and SDR10 associated with Sh resistance. The candidate genes may facilitate simultaneous selection for Sh and Sa resistance and grain yield in maize after further validation and introgression in breeding pipelines. Overall, we recommend breeding maize specifically for resistance to each Striga species using germplasm adapted to the endemic region of each parasite., (© 2024. The Author(s).)

Variable expressivity of disease-associated variants implies a role for secondary variants that modify clinical features. We assessed the effects of modifier variants towards clinical outcomes of 2,252 individuals with primary variants. Among 132 families with the 16p12.1 deletion, distinct rare and common variant classes conferred risk for specific developmental features, including short tandem repeats for neurological defects and SNVs for microcephaly, while additional disease-associated variants conferred multiple genetic diagnoses. Within disease and population cohorts of 773 individuals with the 16p12.1 deletion, we found opposing effects of secondary variants towards clinical features across ascertainments. Additional analysis of 1,479 probands with other primary variants, such as 16p11.2 deletion and CHD8 variants, and 1,084 without primary variants, showed that phenotypic associations differed by primary variant context and were influenced by synergistic interactions between primary and secondary variants. Our study provides a paradigm to dissect the genomic architecture of complex disorders towards personalized treatment., Competing Interests: DECLARATION OF INTERESTS The authors declare no competing interests.

Striga hermonthica (Sh) and S. asiatica (Sa) are major parasitic weeds limiting cereal crop production and productivity in sub-Saharan Africa (SSA). Under severe infestation, Striga causes yield losses of up to 100%. Breeding for Striga-resistant maize varieties is the most effective and economical approach to controlling the parasite. Well-characterized and genetically differentiated maize germplasm is vital to developing inbred lines, hybrids, and synthetic varieties with Striga resistance and desirable product profiles. The objective of this study was to determine the genetic diversity of 130 tropical and sub-tropical maize inbred lines, hybrids, and open-pollinated varieties germplasm using phenotypic traits and single nucleotide polymorphism (SNP) markers to select Striga-resistant and complementary genotypes for breeding. The test genotypes were phenotyped with Sh and Sa infestations using a 13x10 alpha lattice design with two replications. Agro-morphological traits and Striga-resistance damage parameters were recorded under a controlled environment. Further, high-density Diversity Array Technology Sequencing-derived SNP markers were used to profile the test genotypes. Significant phenotypic differences (P<0.001) were detected among the assessed genotypes for the assessed traits. The SNP markers revealed mean gene diversity and polymorphic information content of 0.34 and 0.44, respectively, supporting the phenotypic variation of the test genotypes. Higher significant variation was recorded within populations (85%) than between populations using the analysis of molecular variance. The Structure analysis allocated the test genotypes into eight major clusters (K  =  8) in concordance with the principal coordinate analysis (PCoA). The following genetically distant inbred lines were selected, displaying good agronomic performance and Sa and Sh resistance: CML540, TZISTR25, TZISTR1248, CLHP0303, TZISTR1174, TZSTRI113, TZDEEI50, TZSTRI115, CML539, TZISTR1015, CZL99017, CML451, CML566, CLHP0343 and CML440. Genetically diverse and complementary lines were selected among the tropical and sub-tropical maize populations that will facilitate the breeding of maize varieties with Striga resistance and market-preferred traits., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Dossa et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Trait heritability and the response to selection depend on genetic variation, a prerequisite to developing sorghum varieties with desirable agronomic traits and high carbon sequestration for sustainable crop production and soil health. The present study aimed to assess the extent of genetic variability and associations among agronomic and carbon storage traits in selected sorghum genotypes to identify the best candidates for production or breeding. Fifty genotypes were evaluated at Ukulinga, Bethlehem and Silverton sites in South Africa during the 2022/23 growing season. The following agronomic and carbon storage traits were collected: days to 50% heading (DTH), days to 50% maturity (DTM), plant height (PH), total plant biomass (PB), shoot biomass (SB), root biomass (RB), root-to-shoot biomass ratio (RS), grain yield (GY), harvest index (HI), shoot carbon content (SCc), root carbon content (RCc), grain carbon content (GCc), total plant carbon stock (PCs), shoot carbon stock (SCs), root carbon stock (RCs), and root-to-shoot carbon stock ratio (RCs/SCs), and grain carbon stock (GCs). Higher genotypic coefficient of variations (GCVs) were recorded for GY at 45.92%, RB (39.24%), RCs/SCs (38.45), and RCs (34.62). Higher phenotypic coefficient of variations (PCVs) were recorded for PH (68.91%), followed by GY (51.8%), RB (50.51%), RS (41.96%), RCs/SCs (44.90%), and GCs (41.90%). High broad-sense heritability and genetic advance were recorded for HI (83.76 and 24.53%), GY (78.59 and 9.98%), PB (74.14 and 13.18%) and PCs (53.63 and 37.57%), respectively, suggesting a marked genetic contribution to the traits. Grain yield exhibited positive association with HI (r = 0.76; r = 0.79), DTH (r = 0.13; r = 0.31), PH (r = 0.1; r = 0.27), PB (r = 0.01; r = 0.02), RB (r = 0.05; r = 0.06) based on genotypic and phenotypic correlations, respectively. Further, the path analysis revealed significant positive direct effects of SB (0.607) and RB (0.456) on GY. The RS exerted a positive and significant indirect effect (0.229) on grain yield through SB. The study revealed that PB, SB, RB, RS, RCs, and RCs/SCs are the principal traits when selecting sorghum genotypes with high yield and carbon storage capacity., (© 2024. The Author(s).)

Enlargement of the cerebrospinal fluid (CSF)-filled brain ventricles (cerebral ventriculomegaly), the cardinal feature of congenital hydrocephalus (CH), is increasingly recognized among patients with autism spectrum disorders (ASD). KATNAL2, a member of Katanin family microtubule-severing ATPases, is a known ASD risk gene, but its roles in human brain development remain unclear. Here, we show that nonsense truncation of Katnal2 ( Katnal2Δ 17 ) in mice results in classic ciliopathy phenotypes, including impaired spermatogenesis and cerebral ventriculomegaly. In both humans and mice, KATNAL2 is highly expressed in ciliated radial glia of the fetal ventricular-subventricular zone as well as in their postnatal ependymal and neuronal progeny. The ventriculomegaly observed in Katnal2 Δ17 mice is associated with disrupted primary cilia and ependymal planar cell polarity that results in impaired cilia-generated CSF flow. Further, prefrontal pyramidal neurons in ventriculomegalic Katnal2 Δ 17 mice exhibit decreased excitatory drive and reduced high-frequency firing. Consistent with these findings in mice, we identified rare, damaging heterozygous germline variants in KATNAL2 in five unrelated patients with neurosurgically treated CH and comorbid ASD or other neurodevelopmental disorders. Mice engineered with the orthologous ASD-associated KATNAL2 F244L missense variant recapitulated the ventriculomegaly found in human patients. Together, these data suggest KATNAL2 pathogenic variants alter intraventricular CSF homeostasis and parenchymal neuronal connectivity by disrupting microtubule dynamics in fetal radial glia and their postnatal ependymal and neuronal descendants. The results identify a molecular mechanism underlying the development of ventriculomegaly in a genetic subset of patients with ASD and may explain persistence of neurodevelopmental phenotypes in some patients with CH despite neurosurgical CSF shunting., Competing Interests: Competing interests statement:The authors declare no competing interest.

Sorghum is a vital food and feed crop in the world's dry regions. Developing sorghum cultivars with high biomass production and carbon sequestration can contribute to soil health and crop productivity. The objective of this study was to assess agronomic performance, biomass production and carbon accumulation in selected sorghum genotypes for production and breeding. Fifty sorghum genotypes were evaluated at three locations (Silverton, Ukulinga, and Bethlehem) in South Africa during 2022 and 2023 growing seasons. Significant genotype × location (p < 0.05) interactions were detected for days to 50% heading (DTH), days to 50% maturity (DTM), plant height (PH), total plant biomass (PB), shoot biomass (SB), root biomass (RB), root-to-shoot biomass ratio (RS), and grain yield (GY). The highest GY was recorded for genotypes AS115 (25.08 g plant -1 ), AS251 (21.83 g plant -1 ), and AS134 (21.42 g plant -1 ). Genotypes AS122 and AS27 ranked first and second, respectively, for all the carbon stock parameters except for root carbon stock (RCs), whereas genotype AS108 had the highest RCs of 8.87 g plant -1 . The principal component analysis identified GY, DTH, PH, PB, SB, RB, RCs, RCs/SCs, total plant carbon stock (PCs), shoot carbon stock (SCs), and grain carbon stock (GCs) as the most discriminated traits among the test genotypes. The cluster analysis using agronomic and carbon-related parameters delineated the test genotypes into three genetic groups, indicating marked genetic diversity for cultivar development and enhanced C storage and sustainable sorghum production. The selected sorghum genotypes are recommended for further breeding and variety release adapted to various agroecologies in South Africa., (© 2024. The Author(s).)

Hydrocephalus, characterized by cerebral ventriculomegaly, is the most common disorder requiring brain surgery in children. Recent studies have implicated SMARCC1, a component of the BRG1-associated factor (BAF) chromatin remodelling complex, as a candidate congenital hydrocephalus gene. However, SMARCC1 variants have not been systematically examined in a large patient cohort or conclusively linked with a human syndrome. Moreover, congenital hydrocephalus-associated SMARCC1 variants have not been functionally validated or mechanistically studied in vivo. Here, we aimed to assess the prevalence of SMARCC1 variants in an expanded patient cohort, describe associated clinical and radiographic phenotypes, and assess the impact of Smarcc1 depletion in a novel Xenopus tropicalis model of congenital hydrocephalus. To do this, we performed a genetic association study using whole-exome sequencing from a cohort consisting of 2697 total ventriculomegalic trios, including patients with neurosurgically-treated congenital hydrocephalus, that total 8091 exomes collected over 7 years (2016-23). A comparison control cohort consisted of 1798 exomes from unaffected siblings of patients with autism spectrum disorder and their unaffected parents were sourced from the Simons Simplex Collection. Enrichment and impact on protein structure were assessed in identified variants. Effects on the human fetal brain transcriptome were examined with RNA-sequencing and Smarcc1 knockdowns were generated in Xenopus and studied using optical coherence tomography imaging, in situ hybridization and immunofluorescence. SMARCC1 surpassed genome-wide significance thresholds, yielding six rare, protein-altering de novo variants localized to highly conserved residues in key functional domains. Patients exhibited hydrocephalus with aqueductal stenosis; corpus callosum abnormalities, developmental delay, and cardiac defects were also common. Xenopus knockdowns recapitulated both aqueductal stenosis and cardiac defects and were rescued by wild-type but not patient-specific variant SMARCC1. Hydrocephalic SMARCC1-variant human fetal brain and Smarcc1-variant Xenopus brain exhibited a similarly altered expression of key genes linked to midgestational neurogenesis, including the transcription factors NEUROD2 and MAB21L2. These results suggest de novo variants in SMARCC1 cause a novel human BAFopathy we term 'SMARCC1-associated developmental dysgenesis syndrome', characterized by variable presence of cerebral ventriculomegaly, aqueductal stenosis, developmental delay and a variety of structural brain or cardiac defects. These data underscore the importance of SMARCC1 and the BAF chromatin remodelling complex for human brain morphogenesis and provide evidence for a 'neural stem cell' paradigm of congenital hydrocephalus pathogenesis. These results highlight utility of trio-based whole-exome sequencing for identifying pathogenic variants in sporadic congenital structural brain disorders and suggest whole-exome sequencing may be a valuable adjunct in clinical management of congenital hydrocephalus patients., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Guarantors of Brain. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Introduction: In the face of climate changes and limited water availability for irrigated crop production, enhanced drought tolerance and adaptation is vital to improve wheat productivity. The objective of this study was to determine the responses of newly bred and advanced mutant lines of wheat based on agronomic traits and biomass allocation under drought-stressed and non-stressed environments for production and breeding., Methods: Fifty-three mutant lines, including the parental check and six check varieties, were evaluated under non-stressed (NS) and drought stressed (DS) conditions in the field and controlled environments using a 20 x 3 alpha lattice design with two replicates. The following agronomic data were collected: days to 50% heading (DTH), days to maturity (DTM), plant height (PH), number of productive tillers (PTN), shoot biomass (SB), root biomass (RB), total biomass (TB), root: shoot ratio (RSR), spike length (SL), thousand seeds weight (TSW) and grain yield (GY). Data were analyzed and summarized using various statistical procedures and drought tolerance indices were computed based on grain yield under NS and DS conditions., Results: Significant (P < 0.05) differences were recorded among the mutant lines for most assessed traits under NS and DS conditions. Grain yield positively and significantly (p < 0.001) correlated with PTN (r = 0.85), RB (r = 0.75), SB (r = 0.80), SL (r =0.73), TB (r = 0.65), and TSW (r = 0.67) under DS condition. Principal component analysis revealed three components contributing to 78.55% and 77.21% of the total variability for the assessed agronomic traits under DS and NS conditions, respectively. The following traits: GY, RB, SB, and PTN explained most of the variation with high loading scores under DS condition. Geometric mean productivity (GMP), mean productivity (MP), harmonic mean (HM), and stress tolerance index (STI) were identified as the best drought tolerance indices for the identification of tolerant lines with positive correlations with GY under NS and DS conditions., Discussion: Among the advanced lines tested, LMA16, LMA37, LMA47, LMA2, and LMA42 were selected as the superior lines with high performance and drought tolerance. The selected lines are recommended for multi-environment trails and release for production in water-limited environments in South Africa., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Makebe, Shimelis and Mashilo.)

Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean., Competing Interests: No The authors have declared that no competing interests exist., (Copyright: © 2023 Mwale et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

Pearl millet (Pennisetum glaucum [L.] R. Br.) is a nutrient-dense, relatively drought-tolerant cereal crop cultivated in dry regions worldwide. The crop is under-researched, and its grain yield is low (< 0.8 tons ha -1 ) and stagnant in the major production regions, including Burkina Faso. The low productivity of pearl millet is mainly attributable to a lack of improved varieties, Striga hermonthica [Sh] infestation, downy mildew infection, and recurrent heat and drought stress. Developing high-yielding and Striga-resistant pearl millet varieties that satisfy the farmers' and market needs requires the identification of yield-promoting genes linked to economic traits to facilitate marker-assisted selection and gene pyramiding. The objective of this study was to undertake genome-wide association analyses of agronomic traits and Sh resistance among 150 pearl millet genotypes to identify genetic markers for marker-assisted breeding and trait introgression. The pearl millet genotypes were phenotyped in Sh hotspot fields and screen house conditions. Twenty-nine million single nucleotide polymorphisms (SNPs) initially generated from 345 pearl millet genotypes were filtered, and 256 K SNPs were selected and used in the present study. Phenotypic data were collected on days to flowering, plant height, number of tillers, panicle length, panicle weight, thousand-grain weight, grain weight, number of emerged Striga and area under the Striga number progress curve (ASNPC). Agronomic and Sh parameters were subjected to combined analysis of variance, while genome-wide association analysis was performed on phenotypic and SNPs data. Significant differences (P < 0.001) were detected among the assessed pearl millet genotypes for Sh parameters and agronomic traits. Further, there were significant genotype by Sh interaction for the number of Sh and ASNPC. Twenty-eight SNPs were significantly associated with a low number of emerged Sh located on chromosomes 1, 2, 3, 4, 6, and 7. Four SNPs were associated with days-to-50%-flowering on chromosomes 3, 5, 6, and 7, while five were associated with panicle length on chromosomes 2, 3, and 4. Seven SNPs were linked to thousand-grain weight on chromosomes 2, 3, and 6. The putative SNP markers associated with a low number of emerged Sh and agronomic traits in the assessed genotypes are valuable genomic resources for accelerated breeding and variety deployment of pearl millet with Sh resistance and farmer- and market-preferred agronomic traits., (© 2023. Springer Nature Limited.)

Bottle gourd [ Lagenaria siceraria (Molina) Standl.]) is a relatively drought-tolerant cucurbit due to the high composition of unique biochemical compositions, including cucurbitacin. The objective of this study was to determine the concentrations of cucurbitacins in bottle gourd and their relationship to drought tolerance. The study assessed 12 bottle gourd accessions grown under two moisture levels (i.e., non-stressed (NS) and drought-stressed (DS)) and three drought stress intensities (i.e., mild, moderate, and severe) using a 12 × 2 × 3 factorial experiment designed in a randomized complete block design with three replications. Control studies were undertaken under glasshouse conditions. The content of cucurbitacins B, E, and I were quantified in leaves and roots using high-performance liquid Cchromatography-mass spectrometry (HPLC-MS). The free radical scavenging activities of pure cucurbitacins B, E, and I were quantified using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and a ferrulic acid power assay (FRAP). Results revealed that cucurbitacins B and I were present in accessions BG-48, BG-58, BG-70, BG-78, BG-79, BG-81, BG-52, and GC in leaves and roots under DS condition. The contents of cucurbitacins B and I were enhanced under increased drought intensity for accessions BG-48, BG-81, and GC. In all the leaf and root samples, cucurbitacin E was not detectable. Based on the DPPH test, pure cucurbitacins I, B, and E reduced free radicals at maximum values of 78, 60, and 66%, respectively. Based on the FRAP assay, pure cucurbitacins I, B, and E had maximum ferric-reducing powers of 67, 62, and 48%. Additionally, cucurbitacin I recorded the highest antioxidant activity compared to cucurbitacins B and E. Increased cucurbitacin accumulation and antioxidant properties indicate their role in minimising cell damage caused by oxidative stress under drought-stressed environments. The present study revealed that cucurbitacins B and I serve as novel biochemical markers for screening drought tolerance in bottle gourd or related cucurbits.

Soybean ( Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200 , Glyma.10g065700 , Glyma.18g297900 , and Glyma.14g009900 , were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana . This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs., Competing Interests: Tha author declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Rani, Raza, Ashfaq, Rizwan, Razzaq, Waheed, Shimelis, Babar and Arif.)

Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers., Significance: Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants., (©2023 The Authors; Published by the American Association for Cancer Research.)

Increasing biomass allocation to the root system may increase soil-organic carbon stocks and confer drought adaptation in water-limited environments. Understanding the genetic bases and inheritance of biomass allocation is fundamental for drought tolerance breeding and soil health. The objective of this study was to determine the general and specific combining ability, maternal effects and the mode of gene action controlling the major yield and biomass allocation related traits in wheat to identify good combiners for breeding and enhanced carbon sequestration. Ten selected wheat genotypes were crossed in a full diallel mating design, and 90 F 2 families were generated and evaluated in the field and greenhouse under drought-stressed and non-stressed conditions. Significant differences were recorded among the tested families revealing substantial variation for plant height (PH), kernels per spike (KPS), root biomass (RB), shoot biomass (SB), total plant biomass (PB) and grain yield (GY). Additive gene effects conditioned PH, SB, PB and GY under drought, suggesting the polygenic inheritance for drought tolerance. Strong maternal and reciprocal genetic effects were recorded for RB across the testing sites under drought-stressed conditions. Line BW162 had high yield and biomass production and can be used to transfer favourable genes to its progeny. The parental line LM75 maintained the general combining ability (GCA) effects in a positive and desirable direction for SB, PB and GY. Early generation selection using PH, SB, PB and GY will improve drought tolerance by exploiting additive gene action under drought conditions. Higher RB production may be maintained by a positive selection of male and female parents to capture the significant maternal and reciprocal effects found in this study., (© 2023. The Author(s).)

Assessing the genetic diversity and population structure of cultivated sorghum is important for heterotic grouping, breeding population development, marker-assisted cultivar development, and release. The objectives of the present study were to assess the genetic diversity and deduce the population structure of 200 sorghum accessions using diversity arrays technology (DArT)-derived single nucleotide polymorphism (SNP) markers. The expected heterozygosity values ranged from 0.10 to 0.50 with an average of 0.32, while the average observed heterozygosity (0.15) was relatively low, which is a typical value for autogamous crops species like sorghum. Moderate polymorphic information content (PIC) values were identified with a mean of 0.26, which indicates the informativeness of the chosen SNP markers. The population structure and cluster analyses revealed four main clusters with a high level of genetic diversity among the accessions studied. The variation within populations (41.5%) was significantly higher than that among populations (30.8%) and between samples within the structure (27.7%). The study identified distantly related sorghum accessions such as SAMSORG 48, KAURA RED GLUME; Gadam, AS 152; CSRO1, ICNSL2014-062; and YALAI, KAFI MORI. The accessions exhibited wide genetic diversity that will be useful in developing new gene pools and novel genotypes for West Africa sorghum breeding programs.

Sorghum is the most popular crop in arid and semi-arid areas, especially in Sub-Saharan African countries. Genotype effects, environmental and the interaction of genotype by environmental factors have an influence on phenotypic traits. The aim of the study is to identify the relationship between grain yield and other yield-related traits and select the genotypes which perform better in grain yield as well as to examine the association between the uncorrelated phenotypic traits and grain yield via mixed model. The data was generated using a lattice square design. Principal component analysis was used to generate uncorrelated variables for the mixed model. The study revealed that there was a difference in grain yield due to the treatment and there was a pairwise relationship among the phenotypic variables. 77.12% of the total variance of the original phenotypic variables was explained by the first three principal components and decided to use PCAs as input variables for the mixed model. All PCs had significant effects on grain yield as well as grain yield variability due to random effects associated with genotypes, genotype interaction by treatment, and replication within the treatment. The variability of grain yield due to genotype effect was explained about 45.73%, the variation of grain yield due to the interaction of genotype by the treatment was also explained about 39.06% and 1.55% of the variation of grain was explained by replication within treatment. The best performer genotypes recommended for mass production were G40 (Genotype 40), G186 (Genotype 186) and G196 (Genotype 196) without any constraint of environment. The genotypes recommended for mass production under irrigation conditions were G40 (Genotype 40), G62 (Genotype 62) and G192 (Genotype 192). G26 (Genotype 26), G55 (Genotype 55) and G49 (Genotype 49) were the genotypes recommended for mass production under stress conditions. Overall, the study recommends using a mixed model to fit the grain yield, and future work will focus on to evaluate the performance of genotypes under different environments and years of production., Competing Interests: We have no known competing financial interest or personal relationships., (© 2023 The Authors.)

Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0-0.184 (average 0.02), while the expected heterozygosity ranged from 0.20-0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2023 Rani et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The potential yield of maize ( Zea mays L.) and other major crops is curtailed by several biotic, abiotic, and socio-economic constraints. Parasitic weeds, Striga spp., are major constraints to cereal and legume crop production in sub-Saharan Africa (SSA). Yield losses reaching 100% are reported in maize under severe Striga infestation. Breeding for Striga resistance has been shown to be the most economical, feasible, and sustainable approach for resource-poor farmers and for being environmentally friendly. Knowledge of the genetic and genomic resources and components of Striga resistance is vital to guide genetic analysis and precision breeding of maize varieties with desirable product profiles under Striga infestation. This review aims to present the genetic and genomic resources, research progress, and opportunities in the genetic analysis of Striga resistance and yield components in maize for breeding. The paper outlines the vital genetic resources of maize for Striga resistance, including landraces, wild relatives, mutants, and synthetic varieties, followed by breeding technologies and genomic resources. Integrating conventional breeding, mutation breeding, and genomic-assisted breeding [i.e., marker-assisted selection, quantitative trait loci (QTL) analysis, next-generation sequencing, and genome editing] will enhance genetic gains in Striga resistance breeding programs. This review may guide new variety designs for Striga -resistance and desirable product profiles in maize., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Dossa, Shimelis, Mrema, Shayanowako and Laing.)

Physiological and complementary phenotypic traits are essential in the selection of drought-adapted crop genotypes. Understanding the physiological response of diverse okra genotypes under drought stress conditions is critical to the selection of drought-tolerant accessions for production or breeding. The objective of this study was to assess the levels of drought tolerance in preliminarily selected okra accessions based on leaf gas exchange and chlorophyll fluorescence to determine best-performing genotypes for drought-tolerance breeding. Twenty-six genetically diverse okra accessions were screened under non-stressed (NS) and drought-stressed (DS) conditions under a controlled glasshouse environment using a 13 × 2 alpha lattice design in three replicates, in two growing seasons. Data were subjected to statistical analyses using various procedures. A significant genotype × water condition interaction effect was recorded for transpiration rate (T), net CO 2 assimilation (A), intrinsic water use efficiency (WUE i ), instantaneous water use efficiency (WUE ins ), minimum fluorescence ( Fo' ), maximum fluorescence ( Fm '), maximum quantum efficiency of photosystem II photochemistry ( Fv'/Fm' ), the effective quantum efficiency of PSII photochemistry ( ɸPSII) , photochemical quenching ( qP ), nonphotochemical quenching ( qN ) and relative measure of electron transport to oxygen molecules (ETR/A). The results suggested variable drought tolerance of the studied okra accessions for selection. Seven principal components (PCs) contributing to 82% of the total variation for assessed physiological traits were identified under DS conditions. Leaf gas exchange parameters, T, A and WUE i , and chlorophyll fluorescence parameters such as the ɸPSII , Fv'/Fm' , qP , qN , ETR and ETR/A had high loading scores and correlated with WUE i , the ɸPSII , qP and ETR under DS conditions. The study found that optimal gas exchange and photoprotection enhance drought adaptation in the assessed okra genotypes and tested water regimes. Using the physiological variables, the study identified drought-tolerant accessions, namely LS05, LS06, LS07 and LS08 based on high A, T, Fm' , Fv'/Fm' and ETR, and LS10, LS11, LS18 and LS23 based on high AES , Ci , Ci/Ca , WUEi , WUEins , ɸPSII and AES. The selected genotypes are high-yielding (≥5 g/plant) under drought stress conditions and will complement phenotypic data and guide breeding for water-limited agro-ecologies.

The soybean yield is a complex quantitative trait that is significantly influenced by environmental factors. G × E interaction (GEI), which derives the performance of soybean genotypes differentially in various environmental conditions, is one of the main obstacles to increasing the net production. The primary goal of this study is to identify the outperforming genotypes in different latitudes, which can then be used in future breeding programs. A total of 96 soybean genotypes were examined in two different ecological regions: Faisalabad and Tando Jam in Pakistan. The evaluation of genotypes in different environmental conditions showed a substantial amount of genetic diversity for grain yield. We identified 13 environment-specific genotypes showing their maximum grain yield in each environment. Genotype G69 was found to be an ideal genotype with higher grain yield than other genotypes tested in this study and is broadly adapted for environments E1 and E2 and also included in top-yielding genotypes in E3, E4, and E5. G92 is another genotype that is broadly adapted in E1, E3, and E4. In the case of environments, E3 is suggested to be a more ideal environment as it is plotted near the concentric circle and is very informative for the selection of genotypes with high yield. Despite the presence of GEI, advances in DNA technology provided very useful tools to investigate the insight of advanced genotypes. Association mapping is a useful method for swiftly and efficiently investigating the genetic basis of significant plant traits. A total of 26 marker-trait associations were found for six agronomic traits in five environments, with the highest significance ( p -value = 2.48 × 10 -08 ) for plant height and the lowest significance (1.03 × 10 -03 ) for hundred-grain weight. Soybean genotypes identified in the present study could be a valuable source for future breeding programs as they are adaptable to a wide range of environments. Genetic selection of genotypes with the best yields can be used for gross grain production in a wide range of climatic conditions, and it would give an essential reference in terms of soybean variety selection., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Rani, Raza, Ashfaq, Rizwan, Shimelis, Tung and Arif.)

Objective: Autism, schizophrenia, and other clinically distinct neurodevelopmental psychiatric disorders (NPDs) have shared genetic etiologies, including single-gene and multigenic copy number variants (CNVs). Because rare variants are primarily investigated in clinical cohorts, population-based estimates of their prevalence and penetrance are lacking. The authors determined the prevalence, penetrance, and NPD risk of pathogenic single-gene variants in a large health care system population., Methods: The authors analyzed linked genomic and electronic health record (EHR) data in a subset of 90,595 participants from Geisinger's MyCode Community Health Initiative, known as the DiscovEHR cohort. Loss-of-function pathogenic variants in 94 high-confidence NPD genes were identified through exome sequencing, and NPD penetrance was calculated using preselected EHR diagnosis codes. NPD risk was estimated using a case-control comparison of DiscovEHR participants with and without NPD diagnoses. Results from single-gene variant analyses were also compared with those from 31 previously reported pathogenic NPD CNVs., Results: Pathogenic variants were identified in 0.34% of the DiscovEHR cohort and demonstrated a 34.3% penetrance for NPDs. Similar to CNVs, sequence variants collectively conferred a substantial risk for several NPD diagnoses, including autism, schizophrenia, and bipolar disorder. Significant NPD risk remained after participants with intellectual disability were excluded from the analysis, confirming the association with major psychiatric disorders in individuals without severe cognitive deficits., Conclusions: Collectively, rare single-gene variants and CNVs were found in >1% of individuals in a large health care system population and play an important contributory role in mental health disorders. Diagnostic genetic testing for pathogenic variants among symptomatic individuals with NPDs could improve clinical outcomes through early intervention and anticipatory therapeutic support.

Knowledge of fall armyworm (FAW) (Spodoptera frugiperda J.E. Smith) rearing, infestation and development and precision screening protocols are preconditions for the successful introgression of resistance genes into farmer-preferred varieties. We aimed to determine FAW developmental stages, screen tropical maize and select resistant lines under controlled conditions in Zambia. Field-collected FAW samples constituting 30 egg masses and 60 larvae were reared using maize leaf- and stalk-based and soy- and wheat flour-based diets at 27 ± 1 °C, 60 ± 5% relative humidity and 12 h day length. The resulting neonates were separated into sets A and B. The life cycles of set A and field-collected larvae were monitored to document the FAW developmental features. Set B neonates were used to infest the seedlings of 63 diverse tropical maize genotypes. Egg, larva, pupa and adult stages had mean durations of 2, 24, 20 and 12 days, respectively. Test maize genotypes revealed significant differences (p < 0.05) based on FAW reaction types, with lines TL13159, TL02562, TL142151, VL050120 and CML548-B exhibiting resistance reactions, while CML545-B, CZL1310c, CZL16095, EBL169550, ZM4236 and Pool 16 displayed moderate resistance. These genotypes are candidate sources of FAW resistance for further breeding. This study will facilitate controlled FAW rearing for host screening in the integration of FAW resistance into market-preferred maize lines.

Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations., Competing Interests: The authors of this manuscript declare no conflict of interest.

Purpose: Neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and autism spectrum disorder (ASD), exhibit genetic and phenotypic heterogeneity, making them difficult to differentiate without a molecular diagnosis. The Clinical Genome Resource Intellectual Disability/Autism Gene Curation Expert Panel (GCEP) uses systematic curation to distinguish ID/ASD genes that are appropriate for clinical testing (ie, with substantial evidence supporting their relationship to disease) from those that are not., Methods: Using the Clinical Genome Resource gene-disease validity curation framework, the ID/Autism GCEP classified genes frequently included on clinical ID/ASD testing panels as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship., Results: As of September 2021, 156 gene-disease pairs have been evaluated. Although most (75%) were determined to have definitive roles in NDDs, 22 (14%) genes evaluated had either Limited or Disputed evidence. Such genes are currently not recommended for use in clinical testing owing to the limited ability to assess the effect of identified variants., Conclusion: Our understanding of gene-disease relationships evolves over time; new relationships are discovered and previously-held conclusions may be questioned. Without periodic re-examination, inaccurate gene-disease claims may be perpetuated. The ID/Autism GCEP will continue to evaluate these claims to improve diagnosis and clinical care for NDDs., Competing Interests: Conflict of Interest A.Br. is a shareholder of and employed by Natera. A.Br. has also been an employee of Invitae and Quest Diagnostics commercial laboratories. A.R.C. and K.B. are shareholders of and employed by Illumina, Inc. A.Be. is a shareholder of and is employed by Invitae. B.B. has received research support from Biomarin Pharmaceuticals Inc. He is currently employed by and is a shareholder of Alnylam Pharmaceuticals, Inc. All other authors declare no conflicts of interest., (Copyright © 2022 American College of Medical Genetics and Genomics. Published by Elsevier Inc. All rights reserved.)

Purpose: Penetrance estimates of Birt-Hogg-Dubé syndrome (BHD)-associated cutaneous, pulmonary, and kidney manifestations are based on clinically ascertained families. In a health care system population, we used a genetics-first approach to estimate the prevalence of pathogenic/likely pathogenic (P/LP) truncating variants in FLCN, which cause BHD, and the penetrance of BHD-related phenotypes., Methods: Exomes from 135,990 patient-participants in Geisinger's MyCode cohort were assessed for P/LP truncating FLCN variants. BHD-related phenotypes were evaluated from electronic health records. Association between P/LP FLCN variants and BHD-related phenotypes was assessed using Firth's logistic regression., Results: P/LP truncating FLCN variants were identified in 35 individuals (1 in 3234 unrelated individuals), 68.6% of whom had BHD-related phenotype(s), including cystic lung disease (65.7%), pneumothoraces (17.1%), cutaneous manifestations (8.6%), and kidney cancer (2.9%). A total of 4 (11.4%) individuals had prior clinical BHD diagnoses., Conclusion: In this health care population, the frequency of P/LP truncating FLCN variants is 60 times higher than the previously reported prevalence. Although most variant-positive individuals had BHD-related phenotypes, a minority were previously clinically diagnosed, likely because cutaneous manifestations, pneumothoraces, and kidney cancer were observed at lower frequencies than in clinical cohorts. Improved clinical recognition of cystic lung disease and education concerning its association with FLCN variants could prompt evaluation for BHD., Competing Interests: Conflict of Interest D.H.L is an employee of Unified Patient Network, Inc and scientific consultant for Natera, Inc; MyOme, Inc; and Seven Bridges Genomics. All other authors declare no conflicts of interest., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)

Knowledge of the genetic diversity and genetic relationship is important in crop improvement. The objective of this study was to determine the genetic diversity of 31 sweetpotato genotypes and furthermore to select distantly related individuals for breeding of superior parental clones. The genotypes (sourced from the Agricultural Research Council, South Africa) originating from Africa and American continent were genotyped using eight highly polymorphic SSR markers. The SSR markers generated a total of 83 putative alleles. The polymorphic information content (PIC) of the tested simple sequence markers varied from 0.73 to 0.91, with a mean of 0.85. At least 11 different alleles were found in 8 loci within the population, with 7 effective alleles per locus. Although high diversity was found among the genotypes, genetic distances among the genotypes were relatively low. Cluster analysis revealed the existence of three distinct genetic groups, and the clustering patterns follow to some extent the geographic origin and pedigree of the genotypes. High gene flow was observed among different sweetpotato accessions. The selected SSR markers were found to be highly polymorphic with high discriminatory power for genetic characterization studies and are useful genomic tool to complement phenotyping of sweetpotato genotypes. Two heterotic groups were found in the study. The heterotic group A was composed of 14 genotypes mainly of South African origin, while the heterotic group B consisted of 17 genotypes of American origin. The two distinct groups were important for the selection of breeding clones that were distantly related to be used as parental clones in the advancement of traits of interest.