MapChart: software for the graphical presentation of linkage maps and QTLs

Genome-wide identification and expression patterns of uridine diphosphate (UDP)-glycosyltransferase genes in the brown planthopper, Nilaparvata lugens

Uridine diphosphate-glycosyltransferases (UGTs) are responsible for glycosylation by combining various small lipophilic molecules with sugars to produce water-soluble glycosides, which are crucial for the metabolism of plant secondary metabolites and detoxification in insects. This study presents a genome-wide analysis of the UGT gene family in the brown planthopper, Nilaparvata lugens, a destructive insect pest of rice in Asia. Based on the similarity to UGT homologs from other organisms, 20 putative NlUGT genes were identified in N. lugens. Sequence analysis revealed an average amino acid identity of 45.64 %; however, catalytic and sugar-binding residues, along with UGT signature motifs, were highly conserved. Phylogenetic analysis showed that the 20 NlUGTs were clustered into three main groups. The motif numbers ranged from 5 to 10, with motifs 1 and 4 being found in the functional domains of all 20 NlUGT proteins. Tandem and segmental duplication analysis identified one tandem duplication pair (UGT386K7 and UGT386K8) and two pairs of collinearity genes (UGT362C6/UGT386J4 and UGT386C2/UGT386G5) that expanded through segmental duplication within the UGT gene family of N. lugens. Combining the transcriptome and real-time quantitative PCR data showed that gut, antennae, integument, and ovaries were the tissues enriched with NlUGT gene expression. Six NlUGTs were present mainly in the gut, suggesting their putative roles in detoxification. This research provides valuable information on the molecular and genetic basis of NlUGTs, establishing a solid foundation for subsequent functional investigations of UGTs in planthopper, as well as paving the way for identifying potential targets to manage N. lugens effectively.

Temporal Gene Expression Profiles From Pollination to Seed Maturity in Sorghum Provide Core Candidates for Engineering Seed Traits

Sorghum (Sorghum bicolor (L.) Moench) is a highly nutritional multipurpose millet crop. However, the genetic and molecular regulatory mechanisms governing sorghum grain development and the associated agronomic traits remain unexplored. In this study, we performed a comprehensive transcriptomic analysis of pistils collected 1-2 days before pollination, and developing seeds collected -2, 10, 20 and 30 days after pollination of S. bicolor variety M35-1. Out of 31 337 genes expressed in these stages, 12 804 were differentially expressed in the consecutive stages of seed development. These exhibited 10 dominant expression patterns correlated with the distinct pathways and gene functions. Functional analysis, based on the pathway mapping, transcription factor enrichment and orthology, delineated the key patterns associated with pollination, fertilization, early seed development, grain filling and seed maturation. Furthermore, colocalization with previously reported quantitative trait loci (QTLs) for grain weight/size revealed 48 differentially expressed genes mapping to these QTL regions. Comprehensive literature mining integrated with QTL mapping and expression data shortlisted 25, 17 and 8 core candidates for engineering grain size, starch and protein content, respectively.

Genome-wide Identification, Characterization, and Expression Analysis of NHX Genes in Phaseolus vulgaris L. under Salt Stress: An In Silico Approach

BACKGROUND

Climate change is among the major triggering agents of abiotic stresses (e.g., saline stress), culminating in a vulnerability of common bean production systems. In recent decades, important research has identified and characterized genes that can mitigate the adverse effects caused by salt stress; among them, the Na+/H+ antiporters (NHXs) gene stands out. The NHX genes are widely distributed in all organisms and play significant roles in osmotic regulation in plants under salt stress conditions. Genome-wide identification of NHX genes has been performed in several plant species but not in Phaseolus vulgaris L.

METHODS

This study aimed to identify and characterize NHX genes in P. vulgaris L. using a genome-wide analysis approach conducted in silico. The common bean genome revealed nine putative PvNHX genes, and their subcellular localization, phylogenetic relationship, cis-regulatory elements, conserved motifs identification, chromosomal location, expression patterns, and interaction networks were analyzed.

RESULTS

Promoter analysis suggested that PvNHX genes shared hormone-related elements and were light-responsive and stress-responsive. Seven PvNHX genes were under the regulation of five microRNA (miRNA) families. RNA-seq analysis revealed that most PvNHX genes were expressed in response to salt stress. Currently, the most assertive strategy to confront these adversities is to use the information generated by sequencing plants to identify candidate genes that can be introgressed to improve programs in producing resilient cultures.

CONCLUSION

These results can provide valuable information for future studies on the functional mechanism of PvNHX genes in common beans in response to salt stress.

Genome-wide analysis and functional validation of the cotton FAH gene family for salt stress

BACKGROUND

Fatty acid hydroxylases (FAHs) are a family of enzymes that includes fatty acid hydroxylases, carotenoid hydroxylases, and sterol desaturases. Fatty acids are highly important for plants. They are the main source of energy storage and the main component of the cell membrane. Saturated fatty acids can be divided into two categories: saturated fatty acids and unsaturated fatty acids. FAHs play a pivotal role in enhancing plant salt tolerance by modulating fatty acid metabolic pathways, thereby improving cell membrane stability and antioxidant capacity.

RESULTS

In this study, we identified a total of 129 FAH gene family members in four cotton species, namely, Gossypium hirsutum, Gossypium darwinii, Gossypium arboreum, and Gossypium raimondii. The FAH genes were divided into five subgroups via evolutionary analysis. FAH genes located in the same subgroup presented similar gene structures and a consistent distribution of conserved motifs through the analysis of evolutionary trees, gene structures, and conserved motifs. Chromosomal localization analysis of the FAH gene family revealed that it has undergone chromosomal segment duplication events. Analysis of cis-acting elements suggested that the FAH gene may be involved in regulating biotic and abiotic stresses, plant growth and development, signaling pathways, and other physiological processes. The RT‒qPCR results revealed significant differences in the expression levels of FAH gene family members under salt stress conditions compared with those in the control group. Additionally, we successfully silenced Gohir.A03G045300 through VIGS experiments, and the results indicated that the silenced plants were more sensitive to salt stress than the control plants were. This suggests that Gohir.A03G045300 may be involved in the response of cotton to salt stress.

CONCLUSIONS

A total of 129 FAH genes were identified in four Gossypium species through bioinformatics analysis. Gene silencing of FAH members in G. hirsutum revealed that the FAH gene family plays a crucial role in the response of cotton to salt stress.

Discovery and validation of SSR marker-based QTL governing fresh pod yield in dolichos bean (Lablab purpureus L. Sweet)

Identification and validation of quantitative trait loci (QTL) governing desired phenotype of target trait is a prerequisite to implement marker-assisted selection in any crop including dolichos bean. Under this premise, we used two mapping populations (MPs) to detect and cross population validate QTL controlling fresh pod yield. One of the MPs consisted of F2 individuals (MP1) derived from crossing two elite genotypes, the second MP consisted of random RILs (MP2) derived from a different pair of elite genotypes. The MP1 and MP2 were genotyped using polymorphic 86 and 91 SSR markers, respectively and linkage maps were constructed using QTL IciM mapping software. The MP1 and MP2 were phenotyped during 2021 and 2017 rainy and post rainy seasons, respectively for fresh pod yield plant-1 following two-replicated simple lattice design. QTL maps were developed in MP1 and MP2 using genotype and phenotype data. Our results indicated that the estimates of total map length, average map length per linkage group (LG) and average inter-marker distance in MP2 were greater (by at least 1.5 times) than those in MP1. While seven QTLs were detected in MP1, six were detected in MP2 with three QTL exhibiting positive and additive minor effects for fresh pod yield plant-1. We also detected one common minor positive effect QTL across two seasons in MP2 and significant epistatic QTL, whose main effects were non-significant. One each of the seven and six QTL-linked SSR markers detected in MP1 and MP2, respectively were cross-population validated. The implications of these results are discussed in relation to strategies to breed dolichos bean.

Exploring the drought-responsive miRNAs and their corresponding target genes in chickpea root tissue

Chickpea is an important pulse crop globally, with major production in Southeast Asia. However, the production of chickpea is hampered due to various biotic and abiotic stressors. In response to such stressors, microRNAs which are small non-coding regulatory RNA molecules have been observed as key players. The present study evaluates the role of drought-responsive microRNAs in the root tissues of chickpea genotypes contrasting for drought tolerance. This study led to the generation of 146.7 million short-read sequences from small RNA libraries constructed from the root tissues of the two genotypes. Upon analysis, 224 conserved and 155 novel miRNA sequences were identified. The miR156 family was found to be the most abundant among the 51 families identified for the conserved miRNAs. Quantitative real-time PCR (qRT-PCR) was used to validate eleven conserved and six novel miRNAs. The identification of drought-induced expression of specific miRNAs and their related target genes suggests miRNA-mediated response mechanisms in chickpea. Furthermore, this research investigated the role of drought-responsive miRNAs, specifically miR171 and miR166 and their target genes, SCL27 (scarecrow-like protein 27) and ATHB15 (Homeobox-leucine zipper family protein), respectively. The study validated the miR171 and miR166 directed cleavage of SCL27 and ATHB15, respectively, in drought-stressed root tissues using 5´RLM-RACE (5' RNA Ligase-Mediated Rapid Amplification of cDNA Ends) analysis. The study highlights the role of diverse miRNAs in chickpea for mitigating drought.

Genome-Wide Identification of the SWEET Gene Family and Functional Analysis of BraSWEET10 in Winter B. rapa (Brassica rapa L.) Under Low-Temperature Stress

Sugars will eventually be exported transporter (SWEET), a class of glucose transport proteins, is crucial in plants for glucose transport by redistribution of sugars and regulates growth, development, and stress tolerance. Although the SWEET family has been studied in many plants, little is known about its function in winter B. rapa (Brassica rapa L.). Bioinformatics approaches were adopted to identify the SWEET gene (BraSWEETs) family in B. rapa to investigate its role during overwintering. From the whole-genome data, 31 BraSWEET genes were identified. Gene expansion was realized by tandem and fragment duplication, and the 31 genes were classified into four branches by phylogenetic analysis. As indicated by exon-intron structure, cis-acting elements, MEME (Multiple EM for Motif Elicitation) motifs, and protein structure, BraSWEETs were evolutionarily conserved. According to the heat map, 23 BraSWEET genes were differentially expressed during overwintering, revealing their potential functions in response to low-temperature stress and involvement in the overwintering memory-formation mechanism. BraSWEET10 is mainly associated with plant reproductive growth and may be crucial in the formation of overwintering memory in B. rapa. The BraSWEET10 gene was cloned into B. rapa (Longyou-7, L7). The BraSWEET10 protein contained seven transmembrane structural domains. Real-time fluorescence quantitative PCR (qRT-PCR) showed that the BraSWEET10 gene responded to low-temperature stress. BraSWEET10 was localized to the cell membrane. The root length of overexpressing transgenic A. thaliana was significantly higher than that of wild-type (WT) A. thaliana under low temperatures. Our findings suggest that this gene may be important for the adaptation of winter B. rapa to low-temperature stress. Overall, the findings are expected to contribute to understanding the evolutionary links of the BraSWEET family and lay the foundation for future studies on the functional characteristics of BraSWEET genes.

High-resolution genetic and physical mapping reveals a peanut spotted wilt disease resistance locus, PSWDR-1, to Tomato spotted wilt virus (TSWV), within a recombination cold-spot on chromosome A01

BACKGROUND

Peanut (Arachis hypogaea L.) is a vital global crop, frequently threatened by both abiotic and biotic stresses. Among the most damaging biotic stresses is Tomato spotted wilt virus (TSWV), which causes peanut spotted wilt disease resulting in significant yield loss. Developing TSWV-resistant cultivars is crucial to new cultivar release. Previous studies have used a subset of the "S" recombinant inbred line (RIL) population derived from SunOleic 97R and NC94022 and identified quantitative trait loci (QTLs) for resistance to TSWV. These studies utilized different genotyping techniques and found large consistent genomic regions on chromosome A01. The objective of this study was to fine map the QTL and identify candidate genes using the entire population of 352 RILs and high-density, high-quality peanut SNP arrays.

RESULTS

We used both versions of the peanut SNP arrays with five years of disease ratings, and successfully mapped the long-sought peanut spotted wilt disease resistance locus, PSWDR-1. QTL analyses identified two major QTLs, explaining 41.43% and 43.69% of the phenotypic variance within 3.6 cM and 0.28 cM intervals using the peanut Axiom_Arachis-v1 and Axiom_Arachis-v2 SNP arrays, respectively, on chromosome A01. These QTLs corresponded to 295 kb and 235 kb physical intervals. The unique overlap region of these two QTLs was 488 kb. A comparison of the genetic linkage map with the reference genome revealed a 1.3 Mb recombination "cold spot" (11.325-12.646 Mb) with only two recombination events of RIL-S1 and RIL-S17, which displayed contrasting phenotypes. Sequencing of these two recombinants confirmed the cold spot with only five SNPs detected within this region.

CONCLUSIONS

This study successfully identified a peanut spotted wilt disease resistance locus, PSWDR-1, on chromosome A01 within a recombination "cold spot". The PSWDR-1 locus contains three candidate genes, a TIR-NBS-LRR gene (Arahy.1PK53M), a glutamate receptor-like gene (Arahy.RI1BYW), and an MLO-like protein (Arahy.FX71XI). These findings provide a foundation for future functional studies to validate the roles of these candidate genes in resistance and application in breeding TSWV-resistant peanut cultivars.

Fine mapping of the unique Ur-11 gene conferring broad resistance to the rust pathogen of common bean

KEY MESSAGE

Fine mapping positioned the Ur-11 rust resistance gene in common bean to a narrow 9 kb genomic region and enabled the development of a KASP marker tightly linked to Ur-11 for use in gene pyramiding to achieve durable rust resistance. The extensive virulence diversity of the fungal pathogen Uromyces appendiculatus threatens common bean (Phaseolus vulgaris) production. The Ur-11 gene present in the Guatemalan common bean accession PI 181996 conferred resistance to 89 of 90 virulent races of U. appendiculatus. We describe here the fine mapping of Ur-11 and the development and validation of a DNA marker tightly linked to Ur-11. An F2 population from the cross between the susceptible Pinto 114 with the resistant PI 181996 was inoculated with four races of U. appendiculatus. This study established that the rust resistance in PI 181996 was conferred by Ur-11. We then fine mapped Ur-11 using F2 plants and F2:3 families, high-throughput SNP genotyping, SSRs and KASPs marker development, whole-genome sequencing, and local haplotype analysis. Ur-11 was positioned in a narrow 9.01 Kb genomic region on chromosome Pv11 flanked by KASP markers SS322 and SS375. This genomic region included a candidate gene encoding a nucleotide-binding site and leucine rich-repeat domain with pathogen resistance functions. The validation of the SS322 KASP marker was performed on a panel of 206 diverse common bean cultivars that were inoculated with four races of U. appendiculatus. The SS322 marker was 97.5% accurate in identifying the presence of Ur-11 in common bean plants. These results suggest that S322 will be a highly effective molecular marker for the development of common bean cultivars with Ur-11 alone and combining Ur-11 with other rust resistance genes that would confer broad and durable resistance to the hypervirulent bean rust pathogen.

Genomic Insights into Cobweb Disease Resistance in Agaricus bisporus: A Comparative Analysis of Resistant and Susceptible Strains

Agaricus bisporus, a globally cultivated edible fungus, faces significant challenges from fungal diseases like cobweb disease caused by Cladobotryum mycophilum, which severely impacts yield. This study aimed to explore the genetic basis of disease resistance in A. bisporus by comparing the genomes of a susceptible strain (AB7) and a resistant strain (AB58). Whole-genome sequencing of AB7 was performed using PacBio Sequel SMRT technology, and comparative genomic analyses were conducted alongside AB58 and other fungal hosts of C. mycophilum. Comparative genomic analyses revealed distinct resistance features in AB58, including enriched regulatory elements, specific deletions in AB7 affecting carbohydrate-active enzymes (CAZymes), and unique cytochrome P450 (CYP) profiles. Notably, AB58 harbored more cytochrome P450 genes related to fatty acid metabolism and unique NI-siderophore synthetase genes, contributing to its enhanced environmental adaptability and disease resistance. Pan-genome analysis highlighted significant genetic diversity, with strain-specific genes enriched in pathways like aflatoxin biosynthesis and ether lipid metabolism, suggesting distinct evolutionary adaptations. These findings provide valuable insights into the genetic basis underlying disease resistance in A. bisporus, offering a foundation for future breeding strategies to improve fungal crop resilience.

A novel trait to reduce the mechanical damage of peach fruits at harvest: The first genetic dissection study for peduncle length

In peach, a long peduncle can help minimize mechanical damages/physical injuries in the fruit at harvest and can also be useful in postharvest handling and transportation. In view of genetically dissecting the peduncle length (PL) in peach, we have performed a Quantitative Trait Locus (QTL) mapping study for PL using a F2 progeny of 117 individuals from the cross 'PI 91459 [NJ Weeping]' x 'Bounty' (WxBy). The progeny was phenotyped for three years (2011, 2012 and 2014) and the QTL mapping analysis was performed using four methods: Kruskall-Wallis, Interval Mapping, Multiple QTL Mapping and Genome-Wide Composite Interval Mapping. QTL analysis led to the identification of 9 QTLs distributed on linkage groups (LG) 1, 2, 4, 5, 6 and 7. A stable QTL was identified on LG6 (22,978,897 to 24,666,094 bp) and explained up to 63% of the phenotypic variance. Within the genetic interval of the stable QTL on LG6 potential candidate genes with functional annotation encompassing cellular expansion, hormone regulation, transcriptional regulation, developmental processes such as meristem development, and responses to environmental cues were found. The results reported in this study represent the first insight into the genetic basis of PL and a step forward towards the introduction of novel traits in peach commercial breeding in order to minimize the problems related to mechanical damage/injuries to peach fruits that commonly might occur during at harvest and post-harvest processes.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-025-01547-3.

Characterization of a new Lr52 allele for leaf rust resistance in the Iranian wheat landrace PI 622111

Leaf rust, caused by Puccinia triticina (Pt), poses a constant threat to global wheat production, and novel leaf rust resistance genes are needed to combat the disease. A previous genome-wide association study (GWAS) identified a single nucleotide polymorphism (SNP) marker associated with leaf rust resistance in the terminal region of chromosome arm 5BS in the Iranian landrace PI 622111. An F2 population and 175 F2:3 families from cross PI 622111 × Yuanyu 3 were evaluated for response to Pt isolate Pt52-2 (MMPSD). Genotyping-by-sequencing analysis and genotyping of a subset of the F2 plants identified 32 SNPs closely associated with leaf rust resistance in the target region. Some of these SNPs were converted into kompetitive allele-specific polymorphic (KASP) markers and used to genotype the F2 population together with a set of simple sequence repeat (SSR) markers also located in the target genomic region. Linkage analysis delimited the leaf rust resistance gene in PI 622111, designated Lr622111, to a 0.4 Mb interval flanked by Xstars700 (7.22 Mb) and Xstars678 (7.62 Mb) in IWGSC RefSeq v.2.1. An allelism test involving 811 F2 plants indicated that Lr622111 was allelic to Lr52. Since PI 622111 reacted differently from the Lr52 donor to Pt races in the GWAS, Lr622111 is considered a new Lr52 allele conferring a wide spectrum of resistance to current US Pt races. KASP marker Xstars-KASP239, which is 0.9 cM distal to Lr622111, can be widely used to tag Lr622111 in breeding populations.

Differential expression of CCD4(4B) drives natural variation in fruit carotenoid content in strawberry (Fragaria spp.)

Carotenoids are a diverse group of pigments imparting red, orange, and yellow hues to many horticultural plants, also enhancing their nutritional properties and health benefits. In strawberry, the genetic and molecular mechanisms regulating the natural variation of fruit carotenoid composition remain largely unexplored. In this study, we use a population segregating in yellow/white flesh to detect a major quantitative trait locus (QTL), qYellow Flesh-4B, located on chromosome 4B and accounting for 82% of total phenotypic variation. In the QTL interval, specific polymorphisms on the promoter of the carotenoid cleavage dioxygenase CCD4(4B) were associated with yellow flesh, down-regulation of CCD4(4B) during ripening, and increased carotenoid content. The role of CCD4(4B) in carotenoid turnover was further confirmed through transient overexpression in strawberry fruits, which resulted in decreased concentrations of the xanthophylls violaxanthin, lutein, and zeaxanthin. Notably, a -35 C>T single-nucleotide polymorphism (SNP) in the CCD4(4B) promoter was predictive of both CCD4(4B) expression and carotenoid content across a diverse collection of octoploid Fragaria species. These findings provide valuable genetic insights into the natural variation of carotenoid composition and accumulation in strawberry. A high-resolution melting (HRM) DNA test developed in this study offers a rapid and reliable method for predicting high carotenoid content in strawberry fruits, representing a valuable tool for breeding projects aimed at enhancing the nutritional value of this crop.

Phylogeny and Functional Differentiation of the Terpene Synthase Gene Family in Angiosperms with Emphasis on Rosa chinensis

Terpenes are pivotal for plant growth, development, and adaptation to environmental stresses. With the advent of extensive genomic data and sophisticated bioinformatics tools, new insights into the evolutionary dynamics and functional diversification of terpene synthases (TPSs) have emerged. Despite genome-wide identifications of the TPS family in certain species, comprehensive cross-species analyses remain scarce. In this study, we conducted a genome-wide identification and subgroup classification of TPS families across 115 angiosperms with available genomic sequences. Our phylogenomic synteny network analysis elucidated the complex evolutionary history of TPS genes, revealing notable expansions and contractions among subgroups. Specifically, TPS-a showed significant expansion, while TPS-b was variably lost in some Poaceae, indicating adaptive responses. TPS-c maintained considerable conservation across species, whereas TPS-e/f diverged into distinct evolutionary trajectories despite functional overlap, with TPS-e further splitting into two angiosperm-specific clades. The TPS-g subgroup displayed lineage-restricted distribution, primarily in super-rosids and monocots. Notably, TPS-d and TPS-h subgroups were absent in angiosperms. Employing Rosa chinensis as a case study, we identified RcTPS23, a conserved bifunctional terpene synthase, highlighting the utility of cross-species synteny data in functional prediction. This comprehensive analysis elucidates the phylogenetic and functional landscape of TPS subgroups in angiosperms, providing a robust framework for predicting TPS function and guiding further functional investigations.

Genome-Wide Identification and Functional Analysis of AP2/ERF Gene Family in Passiflora edulis Sims

The Apetala2/Ethylene Responsive Factor (AP2/ERF) family represents a critical group of transcription factors in plants, recognized for their roles in growth, development, fruit ripening, and postharvest processes. This study aimed to identify and characterize the AP2/ERF gene family in passion fruit (Passiflora edulis Sims) and investigate their potential roles in flavor enhancement. A total of 91 PeAP2/ERF genes were identified and classified into five subfamilies. Chromosome localization and collinearity analysis demonstrated their distribution across all nine chromosomes of passion fruit, with tandem duplication events identified as a key driver of family expansion. Exon-intron configurations and motif compositions were highly conserved among PeAP2/ERF genes. Promoter cis-acting element analysis indicated potential regulation by environmental signals, including abiotic and biotic stresses, as well as hormonal cues. Postharvest storage induced the expression of 59 PeAP2/ERF genes over time. Notably, PeAP2-10 was found to enhance the expression of PeSTP6, a gene associated with sugar transport, suggesting its potential influence on the flavor profile of passion fruit. These findings provide valuable insights into the functional roles of PeAP2/ERF genes in passion fruit, highlighting their significance in postharvest management and flavor quality enhancement strategies.

Identification of a New Major Oil Content QTL Overlapped with FAD2B in Cultivated Peanut (Arachis hypogaea L.)

High oil content in peanut seeds is a key breeding objective for peanut (Arachis hypogaea L.) quality improvement. In order to explore the genetic basis of oil content in peanuts, a recombinant inbred line (RIL) population consisting of 256 lines was phenotyped across six environments. Continuous distribution and transgressive segregation for both oil content and oleic acid content were demonstrated across all environments. Quantitative trait locus (QTL) analysis yielded 15 additive QTLs explaining 4.34 to 23.10% of phenotypic variations. A novel stable and major QTL region conditioning oil content (qOCB09.1) was mapped to chromosome B09, spanning a 1.99 Mb genomic region with 153 putative genes, including the oleic acid gene FAD2B, which may influence the oil content. Candidate genes were identified and diagnostic markers for this region were developed for further investigation. Additionally, 18 pairs of epistatic interactions involving 35 loci were identified to affect the oil content, explaining 1.25 to 1.84% of phenotypic variations. These findings provide valuable insights for further map-based cloning of favorable alleles for oil content in peanuts.

Expression profile and characterization of respiratory burst oxidase homolog genes in rice under MeJA, SA and Xoo treatments

Respiratory burst oxidase homologs (Rboh) genes is essential for synthesizing reactive oxygen species, which play a crucial role in environmental stress response. The Rboh gene family has been studied in model plants such as Arabidopsis. Nevertheless, Rboh remained largely unexplored in Rice (Oryza sativa L.). Here, we performed characterization of the Rboh genes family in rice (OsRboh) under Xanthomonas oryzae pv. oryzae (Xoo), salicylic acid (SA), and methyl jasmonate (MeJA) treatments. Nine OsRboh genes were retrieved distributed across six chromosomes (1, 5, 8, 9, 11, 12).These genes vary in amino acid sequence length (728-1034), isoelectric point (9.05-9.84), and molecular weight (8.341-115.014 kDa). Analysis of gene structure, motifs and conserved domains showed that OsRboh genes have similar protein sequences and functions. The promoter region of OsRboh genes was found to contain mainly cis-acting elements associated with light, jasmonic acid (JA), abscisic acid (ABA), and SA responsiveness. Predictions of functional protein-protein interaction showed that OsRboh genes were associated with MAPK signaling, plant-pathogen interaction, and other mRNA surveillance pathways. Prediction of miRNA targets and post-translational modification sites indicated that OsRboh genes may be regulated by miRNA and protein phosphorylation. Phylogenetic analysis showed that OsRboh genes were distributed into 7 clusters. Furthermore, 9 OsRboh genes were differentially expressed in different tissues (roots, stems, and leaves). OsRbohA, OsRbohB, and OsRbohD are significant genes in rice defense responses, showing unique and increased expression profiles under (Xoo-PXO99), (MeJA), and (SA) treatments. These genes important function in triggering defense mechanisms is further stressed by the high (> 20-fold) changes in expression they exhibit under these treatments. These findings enhance our understanding of rice OsRboh genes functions and contribute to stress tolerance improvement strategies.

Mapping and validation of QTkw.cau-3DL, a major QTL controlling thousand-kernel weight in wheat

KEY MESSAGE

A novel major QTL, QTkw.cau-3DL, for thousand-kernel weight has been identified on the wheat chromosome arm 3DL and enhances grain yield by 6.2% under field conditions. Increasing kernel weight is an effective way to improve yield potential in wheat. The identification of major quantitative trait loci (QTL) for kernel weight, without negative effects on other yield-related traits, is crucial for continuous yield improvement. We developed a population of F6 recombinant inbred lines from Jimai 120 × Jimai 325 and identified eight QTL for thousand-kernel weight, kernel length, and kernel width across five environments. The population was genotyped using Wheat15K SNP arrays and QTL analysis found that one QTL, QTkw.cau-3DL, on the chromosome arm 3DL consistently showed major effects on TKW and KL in five field experiments. This QTL accounted for up to 16.43% and 13.87% of phenotypic variation, respectively. QTkw.cau-3DL was confined to a 5.72-Mb (3.48 cM) interval between 554.39 Mb and 560.11 Mb. This QTL was validated in a pair of NILs and in a new population. QTkw.cau-3DL increased kernel weight per spike without any negative effect on heading data, plant height, spike length, spikelet number per spike, or kernels number per spike. It increased grain yield by 6.2% under regular field production conditions. Haplotype analysis and geographical distribution in a nationwide collection of 630 wheat cultivars showed that QTkw.cau-3DL has not been widely deployed in Chinese wheat breeding programs. QTkw.cau-3DL is a novel QTL for increasing TKW through increasing KL; therefore, it is an important locus for enhancing wheat grain yield. The tightly linked, user-friendly markers developed in this study should facilitate map-based cloning and marker-assisted selection of the QTL in wheat breeding programs.

Global identification of metal ion transporters in chickpea and delineating the role of CaYSL4 in orchestrating iron content

Metal ion transporters (MITs) are vital to maintain proper metal homeostasis during growth and development of plants thereby necessitating their identification and characterization. Considering the economic importance of chickpea in human nutrition, the molecular behaviour and biological functions of the metal ion transporters (MIT) encoding gene families remains highly relevant in recent times. Global identification of MITs revealed a total of 12 CAXs, 6 CTRs, 11 MGTs, 15 MTPs, 9 NRAMPs, 16 OPTs, and 14 ZIPs responsible for metal ion transport. Assessment of phylogenetic relationships, chromosomal distribution, gene structure and motif analysis of MITs suggested their diverse functions. The yellow stripe-like (YSL) family of transporters is an important family whose members have been suggested to have a role in metal ion translocation and assimilation. Expression analysis of key YSLs including CaYSL1, CaYSL4, CaYSL6 and CaYSL16 indicated their significant involvement in conferring tolerance to Fe starvation. Notable was the expression of CaYSL4 that showed specific expression in flower, leaf, shoot, seed at 30 DAA and 40DAA after 7 and 10 day of Fe-deficiency treatment. It was found to be localized in the plasma membrane. RNAi-mediated silencing of CaYSL4 demonstrated its critical role in orchestrating Fe, Zn, Cu and Mn translocation in chickpea seeds. Collectively, the comprehensive analysis of MITs coupled with the functional role of CaYSL4 provides critical insight into the complex regulation of Fe ion transport and distribution that will enable breeding of nutritionally enhanced chickpea varieties.

Natural variation in GhROPGEF5 contributes to longer and stronger cotton fibers

Length and strength are key parameters impacting the quality of textiles that can be produced from cotton fibers, and therefore are important considerations in cotton breeding. Through map-based cloning and function analysis, we demonstrated that GhROPGEF5, encoding a ROP guanine nucleotide exchange factor, was the gene controlling fiber length and strength at qFSA10.1. Evolutionary analysis revealed that a base deletion in the third exon of GhROPGEF5 resulting in superior fiber length and strength was a rare mutation occurring in a tiny percentage of Upland cottons, with reduced fiber yield hindering its spread. GhROPGEF5 interacted with and activated GhROP10. Knockout or mutation of GhROPGEF5 resulted a loss of the ability to activate GhROP10. Knockout of GhROPGEF5 or GhROP10 affected the expression of many downstream genes associated with fiber elongation and secondary wall deposition, prolonged fiber elongation and delayed secondary wall deposition, producing denser fiber helices and increasing fiber length and strength. These results revealed new molecular aspects of fiber development and revealed a rare favorable allele for improving fiber quality in cotton breeding.

Genome-wide analysis of the laccase gene family in Arachis hypogaea and functional characterization of AhLAC63 involved in lignin biosynthesis and abiotic stress

Plant laccases (LACs) play a vital role in lignification and participate in multiple biotic/abiotic stress responses. However, little is known about their role in lignin deposition and stress resistance in cultivated peanut (Arachis hypogaea L.). In this study, 80 putative peanut laccase genes (AhLACs) were identified and clustered into seven distinct phylogenetic groups. While the AhLAC members of group VI were lost, a novel specific group VIII was discovered in peanut. AhLACs within same group generally have similar gene structures and protein motif organizations. Expression pattern and subcellular cellular analysis revealed that AhLAC63 is a candidate gene involved in lignification and abiotic stress response. In addition, introducing AhLAC63 into the Arabidopsis laccase mutant (lac4 lac11) restored its lignin contents and abiotic stress tolerance. Moreover, the overexpression of AhLAC63 significantly altered phenylpropanoid metabolism flux and increased lignin content in peanut hairy roots. This study not only enables the further exploration of LAC biological functions in peanut, but also provides new gene resources for improving stress resistance in crops.

Multicomponent Resistance Responses of Melon to Zucchini Yellow Mosaic Virus

A major resistance gene of the melon accession PI414723 to zucchini yellow mosaic virus (ZYMV) is located at the Zym-1 locus on chromosome 2, but the underlying defense mechanisms are poorly understood. The physiological responses and expression of selected genes at Zym-1 were assessed in PI414723 and in the susceptible genotype Védrantais. Viral titers and the expression of genes related to systemic acquired resistance were evaluated in inoculated (Inoc) and noninoculated (Non-Inoc) portions of the cotyledons at 3, 7, and 10 days after inoculation and in apical leaves at 10 days after inoculation. ZYMV was detected in both portions of the cotyledons but not in the apical leaves of PI414723 plants. Also, ZYMV was recovered in a susceptible zucchini only from Inoc portions at 3 days after inoculation. By contrast, in Védrantais, ZYMV was detected and recovered from all tissues at high concentrations. Starchy local lesions and accumulation of transcripts of the systemic acquired resistance marker genes PR1 and PR4 were also detected in the resistant genotype. Plus, transcripts of one candidate resistance gene analog previously located at Zym-1 and of two melon homologs of restricted tobacco etch virus movement 2 genes located close to Zym-1 accumulated only in PI414723. It is proposed that resistance results from the combined action of the R gene involved in restricting ZYMV replication after a supposed recognition event and of the restricted tobacco etch virus movement genes that impact viral systemic movement to distal apical tissues.

First note of QTL mapping of low vigor traits using the updated F2 'Koroneiki' linkage map of olive

The olive tree (Olea europaea L.), which characterizes the agriculture of the Mediterranean basin, faces challenges adapting to high-density orchards and mechanized cultivation. This study addresses a key issue: controlling tree size to enhance efficiency and manageability in olive cultivation. Utilizing genetic mapping methods, we have identified significant Quantitative Trait Loci (QTL) and candidate genes associated with low-vigor traits in olive trees. Our research on the 'Koroneiki' F2 progeny, which exhibits low vigor traits but remains underutilized in breeding programs, has pinpointed a QTL linked to trunk basal diameter-a trait correlated with plant height based on morphological measurements. Results underscore a strong genetic control of these traits, with a consistent correlation observed over time. We identified two candidate genes - Acid Phosphatase 1, Shikimate O-hydroxycinnamoyltransferase, and a SNP Marker likely associated with Calcium Responsive Proteins - each potentially interacting with plant hormones to influence growth. Controlling olive tree size presents several challenges, including the genetic complexity of polygenic traits like size and vigor, and limited rootstock options. By integrating reference genomes with our genetic analysis, we offer a conceptual advancement that could substantially accelerate breeding timelines compared to traditional approaches. Although genome editing is still a future possibility due to the complexity of olive genetics and the species' recalcitrance to transformation, our study lays a foundational understanding to guide future breeding programs. By targeting the identified candidate genes, this research represents a pivotal step toward selecting new low-vigor genotypes and rootstocks, contributing to innovations in olive cultivation.

Genome-wide investigation of ABCB, PIN, and AUX/LAX gene families and their involvement in the formation of leaf protrusions in Sesamum indicum

Sesamum indicum, a highly esteemed oil crop, has exhibited remarkable value and potential in diverse areas encompassing the economy, food industry, and health. We have observed that there are small protrusions on the leaves of the indehiscent capsule material G1358. No obvious difference was detected on overall auxin content between the leaves of G1358 and LZ1 from metabolomic analysis. However, auxin levels at the base of G1358 leaves were notably higher than in LZ1, suggesting a correlation between the small protrusions at the base and polar auxin transport (PAT). PAT is essential for regulating growth and development across different plant tissues. PAT primarily relies on three families of transporter proteins: ABCB, PIN, and AUX/LAX. However, the ABCB, PIN, and AUX/LAX protein families in Sesamum indicum have not been systematically characterized. Herein, we identified 21 SiABCBs, 11 SiPINs, and 5 SiLAXs in S. indicum. Our analysis indicated that tandem duplications have facilitated the expansion of SiLAX, SiPIN, and SiABCB gene families, which have undergone purifying selection throughout their evolutionary history. Transcriptome screening and RT-qPCR analysis revealed that SiABCB3, SiABCB6, and SiPIN10 positively regulate PAT, whereas SiABCB7 and SiABCB9 negatively regulate PAT in G1358. These regulatory interactions contribute to the formation of small protrusions in G1358 leaves and enhance the rate of photosynthesis. Our findings provide a theoretical foundation for understanding PAT genes and their roles in the environmental adaptation of sesame.

Integration of Genetic and Imaging Data to Detect QTL for Root Traits in Interspecific Soybean Populations

Wild soybean, which has many desirable traits, such as adaptability to climate change-related stresses, is a valuable resource for expanding the narrow genetic diversity of cultivated soybeans. Plants require roots to adapt to different environments and optimize water and nutrient uptake to support growth and facilitate the storage of metabolites; however, it is challenging and costly to evaluate root traits under field conditions. Previous studies of quantitative trait loci (QTL) have been mainly based on cultivated soybean populations. In this study, an interspecific mapping population from a cross between wild soybean 'PI483463' and cultivar 'Hutcheson' was used to investigate QTLs associated with root traits using image data. Our results showed that 39 putative QTLs were distributed across 10 chromosomes (chr.). Seventeen of these were clustered in regions on chr. 8, 14, 15, 16, and 17, accounting for 19.92% of the phenotypic variation. We identified five significant QTL clusters influencing root-related traits, such as total root length, surface area, lateral total length, and number of tips, across five chr., with favorable alleles from both wild and cultivated soybeans. Furthermore, we identified eight candidate genes controlling these traits based on functional annotation. These genes were highly expressed in root tissues and directly or indirectly affected soybean root growth, development, and stress responses. Our results provide valuable insights for breeders aiming to optimize soybean root traits and leveraging genetic diversity from wild soybean species to develop varieties with improved root morphological traits, ultimately enhancing overall plant growth, productivity, and resilience.

Unveiling the genetic architecture of barley embryo: QTL mapping, candidate genes identification and its relationship with kernel size and early vigour

KEYMESSAGE

In this first QTL mapping study of embryo size in barley, novel and stable QTL were identified and candidate genes underlying a significant locus independent of kernel size were identified based on orthologous analysis and comparison of the whole-genome assemblies for both parental genotypes of the mapping population. Embryo, also known as germ, in cereal grains plays a crucial role in plant development. The embryo accounts for only a small portion of grain weight but it is rich in nutrients. Larger embryo translates to a more nutritious grain and larger store of energy reserves, which can benefit seed germination and seedling establishment. However, reports on quantitative trait loci (QTL) affecting embryo size in barley is rare. To understand the genetic basis of embryo size in barley, a population consisting of 201 F9 recombination inbred lines (RILs) was assessed in four environments. Three regions affecting various characteristics of embryo size including embryo length (EL), embryo width (EW) and embryo area (EA) were consistently identified. They located on chromosomes 2H, 4H and 7H, respectively. Among them, the QTL on 7H was not significantly affected by kernel size. Phenotypic variances explained by this QTL for EL, EW and EA were 11.8%, 9.3% and 12.7%, respectively. Taken advantage of the available genomic assemblies of the two parental genotypes, candidate genes for this locus on 7H were identified. In addition, significant correlations between embryo size and early vigour and kernel traits were detected. To our knowledge, the present study is for the first time reporting QTL conferring embryo size by directly measuring the characteristics as quantitative trait in barley, which would broaden our understanding of the genetic basis of barley embryo size and offer valuable targets for future breeding programmes.

Phylogenomic analysis reveals exceptions to the co-evolution of ZAR1 and ZRK immune gene families in plants

BACKGROUND

HOPZ-ACTIVATED RESISTANCE 1 (ZAR1) is a nucleotide-binding leucine-rich repeat (NLR) protein functioning as a recognition hub to initiate effector-triggered immunity against bacterial pathogens. To initiate defense, ZAR1 associates with different HOPZ-ETI-DEFICIENT 1 (ZED1)-Related Kinases (ZRKs) to form resistosomes to indirectly perceive effector-induced perturbations. Few studies have focused on the phylogenomic characteristics of ZAR1 and ZRK immune gene families and their evolutionary relationships. To trace the origin and divergence of ZAR1 and ZRK immune gene families across the plant kingdom, we performed phylogenomic analyses using an extended set of plant genomes.

RESULTS

Genome-wide identification of ZAR1 and ZRK immune gene families by blast similarity searches combined with phylogenetic analysis showed that these two gene families have experienced frequent gene losses in massive lineages. Gene distribution patterns across the plant kingdom revealed that ZAR1 and ZRK emerged after the divergence of most angiosperms from Amborella and before the split of magnoliids, monocots, and eudicots. Co-occurrence of ZAR1-A and ZRKs was found in various plant species belonging to different angiosperm orders, but both genes were found to be absent in chlorophyta, bryophytes, lycophytes, ferns, and gymnosperms. We also detected a large number of concerted gene losses in angiosperms, especially within the orders Fabales, Cucurbitales, Asterales, and Apiales. All analysed monocot genomes thus far examined, except for the aroid Colocasia esculenta, were previously reported to lack both ZAR1-A and ZRKs. Here we now report other exceptions on the concerted ZAR1-A-ZRKs presence-absence pattern within several early diverging monocot lineages, including the genome of Acorus tatarinowii-a species representing the first branching monocot lineage. We also revealed strong variation in ZAR1-A-ZRKs co-occurrence within the asterid order Ericales, suggesting patterns of de-coevolution in angiosperms. Our research further shows that both gene families experienced significant diversification through various duplication events. Additionally, their evolutionary paths have been shaped by frequent gene losses and lineage-specific transposition.

CONCLUSION

This study provides novel findings on the evolution of ZAR1 and ZRK immune gene families across a wide range of plant species, suggesting that more potential exceptions can be expected when expanding the list of sequenced genomes from distinct orders. Our results provide new hypotheses about the origin and diversification of these critical immune genes for future functional studies.

Genome wide identification of MATE and ALMT gene family in lentil (Lens culinaris Medikus) and expression profiling under Al stress condition

BACKGROUND

The membrane transporters viz. multidrug and toxic compound extrusion (MATE) and aluminum-activated malate transporter (ALMT) are associated with aluminum (Al) tolerance by accelerating secretion of organic acids, which can influence nutrient availability and stress response. However, such transporter families have not yet been reported in lentil under Al stress condition.

METHOD AND RESULTS

In this study, 90 MATE and 14 ALMT genes were identified and clustered into four (MATE) and five (ALMT) subfamilies/clades with smaller subgroups. All the MATE and ALMT genes were unevenly dispersed across lentil chromosomes. Duplication analysis suggested that LcMATE gene family has expanded primarily through tandem duplication event. Collinearity of lentil with soybean suggested a close relationship between the MATE genes. The MATE promoter regions harboured many stress responsive as well as Al resistance transcription factor 1 related cis-regulatory elements. Predicted 3D (three-dimensional) structure and molecular docking revealed that 5 LcMATE proteins could bind citrate and contain amino acids related to its secretion via citrate exuding motif and other neighbouring sites. Expression analyses of LcMATE and LcALMT genes were performed using quantitative real-time polymerase chain reaction (qRT-PCR). Six genes namely, LcM1, LcM42, LcM46, LcM47, LcALMT8 and LcALMT14 responded to Al stress with varying levels of expression patterns at different time points (3, 6, 12 and 24 h).

CONCLUSION

Our findings offer thorough details on the MATE and ALMT transporters in lentils and will aid in valuable understanding for future functional studies of these transporters in generating Al tolerant cultivars.

Genome-wide identification of HbVQ proteins and their interaction with HbWRKY14 to regulate the expression of HbSRPP in Hevea brasiliensis

BACKGROUND

Valine-glutamine motif-containing proteins (VQ proteins) play important roles in plant growth, development and response to stress. However, information on the VQ gene family in rubber tree (Hevea brasiliensis Muell. Arg.) is limited.

RESULTS

In this study, a total of 21 VQ protein genes (named HbVQ1 ~ HbVQ21) were identified in rubber trees and divided into six subfamilies. Gene structure analysis revealed that most of HbVQs had no introns except for HbVQ5 and HbVQ20. Gene expression analysis revealed that HbVQ4, 5, and 21 were expressed at relatively high levels in latex. In addition, HbVQ4, 5, and 21 interact with the WRKY transcription factor HbWRKY14. Transient co-expression of HbVQ4 or HbVQ5 and HbWRKY14 resulted in relieved HbWRKY14-mediated transcription inhibition of the gene encoding small rubber particle protein (HbSRPP), whereas transient co-expression of HbVQ21 and HbWRKY14 resulted in increased HbWRKY14-mediated HbSRPP transcription inhibition.

CONCLUSIONS

In summary, HbVQ4, 5, and 21 interact with HbWRKY14 to regulate the expression of HbSRPP. This study provides insight into the functions of VQ proteins in regulating natural rubber biosynthesis.

The Potassium Utilization Gene Network in Brassica napus and Functional Validation of BnaZSHAK5.2 Gene in Response to Potassium Deficiency

Potassium, an essential inorganic cation, is crucial for the growth of oil crops like Brassica napus L. Given the scarcity of potassium in soil, enhancing rapeseed's potassium utilization efficiency is of significant importance. This study identified 376 potassium utilization genes in the genome of B. napus ZS11 through homologous retrieval, encompassing 7 functional and 12 regulatory gene families. These genes are unevenly distributed across 19 chromosomes, and the proteins encoded by these genes are mainly localized in the cell membrane, vacuoles, and nucleus. Microsynteny analysis highlighted the role of small-scale replication events and allopolyploidization in the expansion of potassium utilization genes, identifying 77 distinct types of cis-acting elements within their promoter regions. The regulatory mechanisms of potassium utilization genes were provided by analyses of transcription factors, miRNA, and protein interaction networks. Under low potassium stress, the potassium utilization genes, particularly those belonging to the KUP and CBL families, demonstrate pronounced co-expression. RNA-seq and RT-qPCR analysis identified the BnaZSHAK5.2 gene, which is a high-affinity potassium ion transporter, playing a crucial role in the stress response to potassium deficiency in B. napus, as its expression is strongly induced by low potassium stress. A functional complementation study demonstrates that the BnaZSHAK5.2 gene could rescue the primary root growth of the Athak5 mutant under low potassium conditions, confirming its role in response to low potassium stress by sustaining root development.

Genome-wide identification of the wall-associated kinase gene family and their expression patterns under various abiotic stresses in soybean (Glycine max (L.) Merr)

The wall-associated kinase (WAK) gene family encodes functional cell wall-related proteins. These genes are widely presented in plants and serve as the receptors of plant cell membranes, which perceive the external environment changes and activate signaling pathways to participate in plant growth, development, defense, and stress response. However, the WAK gene family and the encoded proteins in soybean (Glycine max (L.) Merr) have not been systematically investigated. In this study, the soybean WAK genes (GmWAK) were identified based on genome-wide sequence information, the basic characteristics, chromosome location, gene replication, expression pattern, and responses to stress were comprehensively analyzed. A total of 74 GmWAK genes were identified and mapped to 19 different chromosomes in the soybean genome. Seventy-four GmWAK genes were divided into four groups, and GmWAK genes in the same group shared similar gene structures and conserved motifs. Thirty-seven duplicate pairs were identified in 74 GmWAK genes. Segmental duplication (SD) was critical in soybean WAK gene family expansion, and purification selection occurred during evolution. The promoter cis-element analysis displayed many hormone- and stress-related response elements in the promoter regions of GmWAK genes. GmWAK genes were diversely expressed in different organs and tissues, with most actively responding to cold, heat, salt, drought, and heavy metal stresses, suggesting that GmWAK genes could exhibit relevant roles in various bioprocesses.

Unveiling the Role of GhP5CS1 in Cotton Salt Stress Tolerance: A Comprehensive Genomic and Functional Analysis of P5CS Genes

Proline, a critical osmoregulatory compound, is integral to various plant stress responses. The P5CS gene, which encodes the rate-limiting enzyme in proline biosynthesis, known as ∆1-pyrroline-5-carboxylate synthetase, is fundamental to these stress response pathways. While the functions of P5CS genes in plants have been extensively documented, their specific roles in cotton remain inadequately characterized. In this study, we identified 40 P5CS genes across four cotton species with diverse sequence lengths and molecular weights. Phylogenetic analysis of 100 P5CS genes from nine species revealed three subgroups, with Gossypium hirsutum closely related to Gossypium barbadense. Collinearity analysis highlighted significant differences in collinear gene pairs, indicating evolutionary divergence among P5CS genes in tetraploid and diploid cotton. Exon-intron structures and conserved motifs correlated with phylogenetic relationships, suggesting functional differentiation. Stress-responsive elements in P5CS promoters suggest involvement in abiotic stress. Expression analysis under salt stress revealed differential expressions of GhP5CS genes, with GhP5CS1 emerging as a potential key regulator. Virus-induced gene silencing confirmed the pivotal role of GhP5CS1 in cotton's salt stress response, as evidenced by increased salt sensitivity in the silenced plants. This study enhances our understanding of the functional diversity and roles of P5CS genes in cotton under stress conditions.

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Single-nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost effective, flexible, and user-friendly. In this study, a new GenoBaits WheatSNP16K (GBW16K) GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies. The GBW16K array contains 14 868 target SNP regions that are evenly distributed across the wheat genome, and 37 669 SNPs in these regions can be identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions is 0.270, which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci (QTLs). A genetic linkage map, constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco"S" and the Chinese landrace Mingxian169, enables the identification of Yr27, Yr30, and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco"S" and of Yr18 from Mingxian169. QYr.nwafu-2BL.4 is different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis, micro-collinearity, gene annotation, RNA sequencing, and SNP data. This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.

Quantitative Trait Loci for Phenology, Yield, and Phosphorus Use Efficiency in Cowpea

BACKGROUND/OBJECTIVES

Cowpea is an important legume crop in sub-Saharan Africa (SSA) and beyond. However, access to phosphorus (P), a critical element for plant growth and development, is a significant constraint in SSA. Thus, it is essential to have high P-use efficiency varieties to achieve increased yields in environments where little-to- no phosphate fertilizers are applied.

METHODS

In this study, crop phenology, yield, and grain P efficiency traits were assessed in two recombinant inbred line (RIL) populations across ten environments under high- and low-P soil conditions to identify traits' response to different soil P levels and associated quantitative trait loci (QTLs). Single-environment (SEA) and multi-environment (MEA) QTL analyses were conducted for days to flowering (DTF), days to maturity (DTM), biomass yield (BYLD), grain yield (GYLD), grain P-use efficiency (gPUE) and grain P-uptake efficiency (gPUpE).

RESULTS

Phenotypic data indicated significant variation among the RILs, and inadequate soil P had a negative impact on flowering, maturity, and yield traits. A total of 40 QTLs were identified by SEA, with most explaining greater than 10% of the phenotypic variance, indicating that many major-effect QTLs contributed to the genetic component of these traits. Similarly, MEA identified 23 QTLs associated with DTF, DTM, GYLD, and gPUpE under high- and low-P environments. Thirty percent (12/40) of the QTLs identified by SEA were also found by MEA, and some of those were identified in more than one P environment, highlighting their potential in breeding programs targeting PUE. QTLs on chromosomes Vu03 and Vu08 exhibited consistent effects under both high- and low-P conditions. In addition, candidate genes underlying the QTL regions were identified.

CONCLUSIONS

This study lays the foundation for molecular breeding for PUE and contributes to understanding the genetic basis of cowpea response in different soil P conditions. Some of the identified genomic loci, many being novel QTLs, could be deployed in marker-aided selection and fine mapping of candidate genes.

The haplotype-phased genome assembly facilitated the deciphering of the bud dormancy-related QTLs in Prunus mume

Bud dormancy is a vital physiological process in woody perennials, facilitating their adaptation to seasonal environmental changes. Satisfying genotype-specific chilling requirements (CR) and heat requirements (HR) through exposure to specific chilling and warm temperatures is essential for dormancy release and the subsequent resumption of growth. The genetic mechanisms regulating bud dormancy traits in Prunus mume remain unclear. In this study, we first assembled the genome of 'Nanko', the leading P. mume cultivar in Japan, in a haplotype-resolved manner. Using an F1 segregating population from a cross between 'Nanko' (high-chill) and 'SC' (low-chill), a cultivar adapted to subtropical conditions, we identified quantitative trait loci (QTLs) for vegetative bud dormancy traits on chromosome 4 (LG4 QTLs) in the 'Nanko' genome and for CR and HR on chromosome 7 (LG7 QTL) in the 'SC' genome. A notable 5.6 Mb chromosome inversion was overlapped with LG4 QTL interval in one of the 'Nanko' haplotypes. We also identified candidate genes based on haplotyping, differential expression between the parents or the presence of trait-correlated variants in coding regions. Notably, genes such as PmuMAIN, PmuNAC2, PmuDOG1, PmuSUI1, PmuATG8CL, PmubZIP44, and PmuSAUR50 were identified. This study provides valuable insights into the genetic regulation of vegetative bud dormancy in Prunus species.

Genome-Wide Identification and Expression Analysis of Members in the YT521-B Homology Domain-Containing RNA Binding Protein Family in Ginkgo biloba

N6-methyladenosine (m6A) is a widespread post-transcriptional modification of RNA in eukaryotes. The conserved YTH-domain-containing RNA binding protein has been widely reported to serve as a typical m6A reader in various species. However, no studies have reported the m6A readers in Ginkgo biloba (G. biloba). In this study, a systematic analysis of the m6A reader (YTH) gene family was performed on G. biloba, identifying 10 YTH genes in its genome. Phylogenetic analysis of protein-coding sequences revealed that YTH genes from G. biloba could be classified into two subgroups: GbDC1 and GbDC2 in GbDC and GbDF1-8 in GbDF, each with similar motifs and gene structures. In G. biloba, the predicated aromatic cage pocket of the YTH domains in the YTH gene family is uniformly composed of tryptophan residues (WWW). Subcellular localization experiments verified that GbDC1 is indeed localized in the nucleus, while GbDF1 is localized in both the nucleus and the cytoplasm. The expression patterns of the identified m6A reader genes showed a wide distribution but were tissue-specific. Most genes were highly expressed in leaves, followed by the stem, while the lowest expression tendency was found in the roots. Cis-regulatory element analysis predicted the possible functions of YTH genes in G. biloba, which were mainly responsive to plant hormones such as ABA and MeJA, as well as stress responses. Furthermore, the expression levels of YTH genes indeed changed significantly after ABA, MeJA, and NaCl treatments, suggesting that they can be affected by these abiotic factors. In addition, the PLAAC prediction results indicate that prion domains exist in GbDF1, GbDF2, GbDF3, GbDF4, GbDF6, GbDF7, GbDF8, and GbDC1, and phase separation is possible. This study provides a foundation for further investigation of the effects of m6A methylation on gene expression regulation in G. biloba and other forest trees.

Characterization of a Major Quantitative Trait Locus for the Whiteness of Rice Grain Using Chromosome Segment Substitution Lines

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC4F2 segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC4F2 population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement.

Salicylic Acid-Induced Expression Profiles of LRR and LRR-RLK Candidate Genes Modulate Mungbean Yellow Mosaic India Virus Resistance in Blackgram and Its Two Wild Non-Progenitors

Blackgram is an important short-duration grain legume, but its yield is highly affected by various stresses. Among biotic stresses, yellow mosaic disease (YMD) is known as a devastating disease that leads to 100% yield loss under severe conditions. The cultivated lines possess resistance, but exploring more diverse sources of resistance may be useful for pyramiding to improve the durability of said resistance. Some wild Vigna species have potentially demonstrated a high level of resistance. R-genes, including gene families of leucine-rich repeats (LRRs) and leucine-rich repeat receptor-like kinases (LRR-RLKs), are known for modulating the resistance in plants against various biotic stresses. The first comprehensive analysis of the LRR and LRR-RLK gene families in mungbean is reported in the present study. A total of forty-six candidate genes were identified and grouped into eight clades. Protein motif analysis showed that the "Pkinase domain" and "LRR domains" were conserved in most of the R-proteins. The expression of candidate genes viz. VrNBS_TNLRR-8, VrLRR_RLK-20, VrLRR_RLK-17, and VrLRR_RLK-19 demonstrated significantly up-regulated expression upon YMD infection in control and salicylic acid-primed (SA-primed) plants. The analysis provides insight into the diversity and robust candidate genes for functional studies modulating YMD resistance altered by salicylic acid.

Multi-omics analysis reveals the evolution, function, and regulatory mechanisms of SPF pheromones in Anurans

Pheromones play a pivotal role in chemical communication across various taxa, with protein-based pheromones being particularly significant in amphibian courtship and reproduction. In this study, we investigate the Emei music frog (Nidirana daunchina), which utilizes both acoustic and chemical signals for communication. Base on a de novo assembled genome of a male Emei music frog, we identify substantial expansion in four pheromone-related gene families associated with chemical communication. Notably, six members of the two-domain three-finger protein (2D-TFP) family, belonging to the sodefrin precursor-like factor (SPF) pheromone system, exhibited high and specific expression in the male post-axillary glands during the breeding season. Structural and evolutionary analyses confirm the presence of the SPF system across amphibians, classifiable into four distinct classes (two within urodeles and two within anurans). We propose a complete regulatory network governing SPF secretion via the hypothalamic-pituitary-testicular-breeding gland axis, and suggest testosterone synthesis as the pivotal pathway. Behavioral experiments further reveal a previously unknown female-attractant role of SPF in anurans. Overall, these findings not only highlight the underestimated diversity and function of pheromones in anurans, but also provide important insights into the evolution of protein-based pheromones in vertebrates.

Genome-wide association study reveals heat tolerance QTL for canopy-closure and early flowering in chickpea

Chickpeas are a vital source of protein and starch for a large portion of the world's population and are known to be impacted by heat stress at every life stage. Previously known as an "Orphan Legume", little is known of the genetic control of heat stress tolerance, and most previous research has focused on heat avoidance rather than tolerance. This study utilised a population of 148 chickpea genotypes, primarily Kabulis, in 12 field trials conducted at 2 locations, two sowing periods, and across 3 years. Physiology was examined, and data was paired with Diversity Arrays Technology (DArT) sequencing to perform a Genome Wide Association Study to connect phenotypic and genotypic regions. Fourteen QTL related to yield, seed size, time to flowering, time to maturity, and final canopy closure were found. Among these, are the first Quantitative Trait Loci (QTL) ever identified for canopy closure in chickpea, along with a QTL that is likely linked to early flowering under heat stress. Early flowering in this case refers to a cultivar flowering significantly earlier than the others in the genotype set. Additionally, several other QTL provide validation of previous research. These QTL hotspots that can be targeted for selective breeding of several traits concurrently. Overall, new targets for genome assisted breeding for heat tolerance in chickpea were identified and can be utilised by the breeder community to improve the status of selective breeding for heat tolerance in this crop.

A Comprehensive Analysis In Silico of KCS Genes in Maize Revealed Their Potential Role in Response to Abiotic Stress

β-ketoacyl-CoA synthase (KCS) enzymes play a pivotal role in plants by catalyzing the first step of very long-chain fatty acid (VLCFA) biosynthesis. This process is crucial for plant development and stress responses. However, the understanding of KCS genes in maize remains limited. In this study, we present a comprehensive analysis of ZmKCS genes, identifying 29 KCS genes that are unevenly distributed across nine maize chromosomes through bioinformatics approaches. These ZmKCS proteins varied in length and molecular weight, suggesting functional diversity. Phylogenetic analysis categorized 182 KCS proteins from seven species into six subgroups, with maize showing a closer evolutionary relationship to other monocots. Collinearity analysis revealed 102 gene pairs between maize and three other monocots, whereas only five gene pairs were identified between maize and three dicots, underscoring the evolutionary divergence of KCS genes between monocotyledonous and dicotyledonous plants. Structural analysis revealed that 20 out of 29 ZmKCS genes are intronless. Subcellular localization prediction and experimental validation suggest that most ZmKCS proteins are likely localized at the plasma membrane, with some also present in mitochondria and chloroplasts. Analysis of the cis-acting elements within the ZmKCS promoters suggested their potential involvement in abiotic stress responses. Notably, expression analysis under abiotic stresses highlighted ZmKCS17 as a potential key gene in the stress response of maize, which presented an over 10-fold decrease in expression under salt and drought stresses within 48 h. This study provides a fundamental understanding of ZmKCS genes, paving the way for further functional characterization and their potential application in maize breeding for enhanced stress tolerance.

Genome-Wide Identification, Functional Characterization, and Stress-Responsive Expression Profiling of Subtilase (SBT) Gene Family in Peanut (Arachis hypogaea L.)

Subtilases (SBTs), known as serine proteases or phytoproteases in plants, are crucial enzymes involved in plant development, growth, and signaling pathways. Despite their recognized importance in other plant species, information regarding their functional roles in cultivated peanut (Arachis hypogea L.) remains sparse. We identified 122 AhSBT genes in the STQ peanut genome, classifying them into six subgroups based on phylogenetic analysis. Detailed structural and motif analyses revealed the presence of conserved domains, highlighting the evolutionary conservation of AhSBTs. The collinearity results indicate that the A. hypogea SBT gene family has 17, 5, and 1 homologous gene pairs with Glycine max, Arabidopsis thaliana, and Zea mays, respectively. Furthermore, the prediction of cis-elements in promoters indicates that they are mainly associated with hormones and abiotic stress. GO and KEGG analyses showed that many AhSBTs are important in stress response. Based on transcriptome datasets, some genes, such as AhSBT2, AhSBT18, AhSBT19, AhSBT60, AhSBT102, AhSBT5, AhSBT111, and AhSBT113, showed remarkably higher expression in diverse tissues/organs, i.e., embryo, root, and leaf, potentially implicating them in seed development. Likewise, only a few genes, including AhSBT1, AhSBT39, AhSBT53, AhSBT92, and AhSBT115, were upregulated under abiotic stress (drought and cold) and phytohormone (ethylene, abscisic acid, paclobutrazol, brassinolide, and salicylic acid) treatments. Upon inoculation with Ralstonia solanacearum, the expression levels of AhSBT39, AhSBT50, AhSBT92, and AhSBT115 were upregulated in disease-resistant and downregulated in disease-susceptible varieties. qRT-PCR-based expression profiling presented the parallel expression trends as generated from transcriptome datasets. The comprehensive dataset generated in the study provides valuable insights into understanding the functional roles of AhSBTs, paving the way for potential applications in crop improvement. These findings deepen our understanding of peanut molecular biology and offer new strategies for enhancing stress tolerance and other agronomically important traits.

The interaction networks of small rubber particle proteins in the latex of Taraxacum koksaghyz reveal diverse functions in stress responses and secondary metabolism

The Russian dandelion (Taraxacum koksaghyz) is a promising source of natural rubber (NR). The synthesis of NR takes place on the surface of organelles known as rubber particles, which are found in latex - the cytoplasm of specialized cells known as laticifers. As well as the enzymes directly responsible for NR synthesis, the rubber particles also contain small rubber particle proteins (SRPPs), the most abundant of which are SRPP3, 4 and 5. These three proteins support NR synthesis by maintaining rubber particle stability. We used homology-based searches to identify the whole TkSRPP gene family and qPCR to create their spatial expression profiles. Affinity enrichment-mass spectrometry was applied to identify TkSRPP3/4/5 protein interaction partners in T. koksaghyz latex and selected interaction partners were analyzed using qPCR, confocal laser scanning microscopy and heterologous expression in yeast. We identified 17 SRPP-like sequences in the T. koksaghyz genome, including three apparent pseudogenes, 10 paralogs arranged as an inverted repeat in a cluster with TkSRPP3/4/5, and one separate gene (TkSRPP6). Their sequence diversity and different expression profiles indicated distinct functions and the latex interactomes obtained for TkSRPP3/4/5 suggested that TkSRPP4 is a promiscuous hub protein that binds many partners from different compartments, whereas TkSRPP3 and 5 have more focused interactomes. Two interactors shared by TkSRPP3/4/5 (TkSRPP6 and TkUGT80B1) were chosen for independent validation and detailed characterization. TkUGT80B1 triterpenoid glycosylating activity provided first evidence for triterpenoid saponin synthesis in T. koksaghyz latex. Based on its identified interaction partners, TkSRPP4 appears to play a special role in the endoplasmic reticulum, interacting with lipidmodifying enzymes that may facilitate rubber particle formation. TkSRPP5 appears to be involved in GTPase-dependent signaling and TkSRPP3 may act as part of a kinase signaling cascade, with roles in stress tolerance. TkSRPP interaction with TkUGT80B1 draws a new connection between TkSRPPs and triterpenoid saponin synthesis in T. koksaghyz latex. Our data contribute to the functional differentiation between TkSRPP paralogs and demonstrate unexpected interactions that will help to further elucidate the network of proteins linking TkSRPPs, stress responses and NR biosynthesis within the cellular complexity of latex.

Identification and characterization of CmPP2C31 playing a positive role in the abiotic stress resistance of Chinese chestnut via an integrated strategy

Chinese chestnut (Castanea mollissima Blume) is an important economic forest tree species and mainly cultivated in mountainous areas and wastelands, subjecting it to various abiotic stresses. The protein phosphatase 2C (PP2C) genes contributes largely to stress responses in plants. However, the characteristics and functions of PP2C genes in C. mollissima remain unknown. This study provides comprehensive analyses (including phylogenetic, synteny, RNA-seq, transgenic and yeast one-hybrid methods) revealing the characteristics of CmPP2C gene, which plays an important role in response to abiotic stress. Here, we identified 68 CmPP2Cs in the Chinese chestnut genome, and analyzed their characteristics and phylogenetic relationships. Furthermore, synteny analysis revealed that segmental and tandem duplication drove the expansion of the CmPP2C family to adapt to natural environmental pressures. RNA sequencing and co-expression analyses indicated that four hub CmPP2Cs in two key modules probably play important roles in the resistance to abiotic stress in chestnut. Among them, CmPP2C31 was significantly down-regulated under drought stress. Transgenic experiments via pollen magnetofection revealed that CmPP2C31 could positively and significantly regulate the drought resistance of Chinese chestnut seedlings. Subcellular localization showed that CmPP2C31 was a nuclear protein. Yeast one-hybrid assays suggested that EVM0007407 could regulate CmPP2C31 expression by binding to its promoter, thereby participating in abiotic stress resistance. These findings in our study provided detailed information on the CmPP2C family genes and laid a foundation for further elucidating the molecular mechanism of resistance to abiotic stress chestnut.

Evolution and comparative transcriptome analysis of glucosinolate pathway genes in Brassica napus L

Glucosinolates (GSLs) are important secondary metabolites abundantly distributed in Brassicaceae plants, whose degradation products benefit plant resistance but are regarded as disadvantageous factors for human health. Thus, reducing GSL content is an important goal in the breeding program in crops, such as Brassica napus. In this study, 1280 genes in the GSL pathway were identified from 14 land plant genomes, which are specifically distributed in Brassicaceae and are extensively expanded in B. napus. Most GSL pathway genes had many positive selection sites, especially the encoding genes of transcription factors (TFs) and structural genes involved in the GSL breakdown process. There are 344 genes in the GSL pathway in the B. napus genome, which are unequally distributed on the 19 chromosomes. Whole-genome duplication mainly contributed to the gene expansion of the GSL pathway in B. napus. The genes in GSL biosynthesis were regulated by various TFs and cis-elements in B. napus and mainly response to abiotic stress and hormone induction. A comparative transcriptome atlas of the roots, stems, leaves, flowers, siliques, and seeds of a high- (ZY821), and a low-GSL-content (ZS11) cultivar was constructed. The features of the two cultivars may be attributed to diverse expression differences in each organ at different stages, especially in seeds. In all, 65 differential expressed genes (DEGs) concentrated on the core structure pathway were inferred to mainly influence the GSL contents between ZY821 and ZS11. This study provides an important RNA-seq dataset and diverse gene resources for future manipulating GSLs biosynthesis and distribution in B. napus using molecular breeding methods.

Comprehensive Analysis of the OASTL Gene Family in Potato (Solanum tuberosum L.) and Its Expression Under Abiotic Stress

O-acetylserine (thiol) lyase is a pivotal enzyme in plant cysteine biosynthesis, which is crucial for promoting plant growth, development, and resisting abiotic stress. However, the related studies on the potato OASTL gene family (StOASTL) have not been reported. In the present study, we identified 11 members of the StOASTL gene family, conducting a thorough analysis encompassing chromosome distribution, protein physicochemical properties, gene structure, protein-conserved motifs, and gene replication events. Phylogenetic scrutiny delineated these 11 StOASTLs into five distinct subfamilies. Using RNA-seq from the Potato Genome Sequencing Consortium (PGSC), we investigated the expression profile of StOASTLs in different tissues of DM (double-monoploid) potato and under abiotic/biotic stress, hormone treatment, and biostimulant treatment. The results showed that one of the StOASTLs (Soltu09G024390) was differentially expressed under different abiotic stresses and hormone treatments. Our findings showcased the differential response of one StOASTL (Soltu09G024390) to a spectrum of abiotic stresses and hormone treatments. Soltu09G024390 was earmarked as a candidate gene and successfully cloned. Functional validation through yeast stress assays demonstrated that the heterologous expression of Soltu09G024390 bolstered yeast tolerance to salt and cadmium stresses. This study provides a theoretical basis for revealing the role of the StOASTL family in potato response to abiotic stress and valuable insights for further study of the biological functions of StOASTL.

Unravelling turbot (Scophthalmus maximus) resistance to Aeromonas salmonicida: transcriptomic insights from two full-sibling families with divergent susceptibility

Introduction

Furunculosis, caused by the gram-negative bacterium Aeromonas salmonicida subsp. salmonicida, remains a significant threat to turbot (Scophthalmus maximus) aquaculture. Identifying genetic backgrounds with enhanced disease resistance is critical for improving aquaculture health management, reducing antibiotic dependency, and mitigating economic losses.

Methods

In this study, five full-sibling turbot families were challenged with A. salmonicida, which revealed one family with significantly greater resistance. Transcriptomic analyses (RNA-Seq) were performed on resistant and susceptible families, examining both naïve and 24-h postinfection (hpi) samples from head kidney and liver tissues.

Results

In the absence of infection, differentially expressed genes (DEGs) were identified predominantly in the liver. Following infection, a marked increase in DEGs was observed in the head kidney, with many genes linked to immune functions. Interestingly, the resistant family displayed a more controlled inflammatory response and upregulation of genes related to antigen presentation and T-cell activity in the head kidney at early infection stages, which may have contributed to its increased survival rate. In the liver, transcriptomic differences between the families were associated mainly with cytoskeletal organization, cell cycle regulation, and metabolic processes, including insulin signalling and lipid metabolism, regardless of infection status. Additionally, many DEGs overlapped with previously identified quantitative trait loci (QTLs) associated with resistance to A. salmonicida, providing further insights into the genetic basis of disease resistance.

Discussion

This study represents the first RNA-Seq analysis comparing resistant and susceptible turbot families and contributes valuable knowledge for the development of selective breeding programs targeting disease resistance in turbot and other aquaculture species susceptible to A. salmonicida.

GenoSee: a novel visualization tool for graphical genotypes

Visualizing genotypic data is essential in genetic research and breeding programs as it offers clear representations of genomic information, enhancing understanding of genetic architecture. This becomes especially critical with the emergence of next-generation sequencing (NGS) technologies, which generate vast datasets necessitating effective visualization tools. While traditional tools for graphical genotypes have been groundbreaking, they often lack flexibility and universal applicability. These tools encounter limitations such as user-customized visualization and compatibility issues across different operating systems. In this study, I introduce GenoSee, a novel visualization tool designed to address these shortcomings. GenoSee can handle phased and non-phased variant calling data, offering extensive customization to suit diverse research requirements. It operates seamlessly across multiple platforms, ensuring compatibility, and provides high-quality graphical genotypes. GenoSee facilitates deeper insights into genomic structures, thereby advancing genetic and genomic research, and breeding programs by enhancing accessibility to genetic data visualization.

Genetic Analysis of Stripe Rust Resistance in the Chinese Wheat Cultivar Luomai 163

Stripe or yellow rust (YR) caused by Puccinia striiformis tritici (Pst) is an important foliar disease affecting wheat production globally. Resistant varieties are the most economically and environmentally effective way to manage this disease. The common winter wheat (Triticum aestivum L.) cultivar Luomai 163 exhibited resistance to the Pst races CYR32 and CYR33 at the seedling stage and showed a high level of adult plant resistance in the field. To understand the genetic basis of YR resistance in this cultivar, 142 F5 recombinant inbred lines (RILs) derived from cross Apav#1 × LM163 and both parents were genotyped with the 16K SNP array and bulked segregant analysis sequencing. The analysis detected a major gene, YrLM163, at the seedling stage associated with the 1BL.1RS translocation. Additionally, three genes for resistance at the adult plant stage were detected on chromosome arms 1BL (Lr46/Yr29/Pm39/Sr58), 6BS, and 6BL in Luomai 163, whereas Apav#1 contributed resistance at a quantitative trait locus (QTL) on 2BL. These QTL explained YR disease severity variations ranging from 6.9 to 54.8%. The kompetitive allele-specific PCR (KASP) markers KASP-2BL, KASP-6BS, and KASP-6BL for the three novel loci QYr.hzau-2BL, QYr.hzau-6BS, and QYr.hzau-6BL were developed and validated. QYr.hzau-1BL, QYr.hzau-2BL, and QYr.hzau-6BS showed varying degrees of resistance to YR when present individually or in combination based on genotype and phenotype analysis of a panel of 570 wheat accessions. Six RILs combining resistance alleles of all QTL, showing higher resistance to YR in the field than Luomai 163 with disease severities of 10.7 to 16.0%, are important germplasm resources for breeding programs to develop YR-resistant wheat varieties with good agronomic traits.

Candidate selective sweeps in US wheat populations

Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using Fst, Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms.