Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

Metabolome guided treasure hunt - learning from metabolic diversity

Metabolomics is a rapidly evolving field focused on the comprehensive identification and quantification of small molecules in biological systems. As the final layer of the biological hierarchy following of the genome, transcriptome and proteome, it presents a dynamic snapshot of phenotype, influenced by genetic, environmental and physiological factors. Whilst the metabolome sits downstream of genes and proteins, there are multiple higher levels-tissues, organs, the entire organism, and interactions with other organisms, which need to be considered in order to fully comprehend organismal biology. Advances in metabolomics continue to expand its applications in plant biology, biotechnology, and natural product discovery unlocking many of nature's most beneficial colors, tastes, nutrients and medicines. Flavonoids and other specialized metabolites are essential for plant defense against oxidative stress and function as key phytonutrients for human health. Recent advancements in gene-editing and metabolic engineering have significantly improved the nutritional value and flavor of crop plants. Here we highlight how advanced metabolic analysis is driving improvements in crops uncovering genes that influence nutrient and flavor profile and plant derived compounds with medicinal potential.

Genome-Wide Identification and Functional Characterization of Brown Spot Resistance Genes in Rice (Oryza sativa L.)

Rice brown spot (BS) caused by Cochliobolus miyabeanus affects both rain-fed and upland rice production, causing both yield and grain quality loss. Here, we used a genome-wide association study (GWAS) to analyze the resistance of 130 rice cultivars to BS disease. We identified two quantitative trait loci on chromosome 4. We screened three candidate genes using two kinds of RNA-seq data, LD block, Gene Ontology, Kyoto Encyclopedia of Genes and Genomes databases (KEGG), and reverse transcription-quantitative polymerase chain reaction. To further identify the candidate gene function, we constructed transgenic lines to verify the gene resistance functions against C. miyabeanus. The gene function research about the overexpression lines of OsExo70F3 and OsBSR820 and the Osmed30 gene function loss T-DNA lines showed more resistance to BS than their wildtypes. The exo70 and Med gene families reportedly participate in abiotic stress in rice, and OsBSR820 is a novel functional gene detected in GWAS-based studies. Subcellular localization results also showed that these genes were located in the cellular sites associated with plant immunity. This is the first study to use GWAS to locate BS resistance genes and to identify the function of genes. We believe that this study will provide valuable insights for exploring additional BS disease resistance-related genes in the future.

Durum wheat nuclear factor Y (NF-Y) a subfamily: structure, phylogeny, and expression analysis in response to hormones and abiotic stresses

Nuclear factor-Y (NF-Y) transcription factors are heterotrimeric complexes that are widely distributed in eukaryotes and play essential roles in many biological processes. Although NF-YA proteins have been characterized in numerous plants, their contribution to the response of durum wheat (Triticum turgidum ssp. durum) to environmental factors has not been reported. Thus, this study was aimed at identification and characterization of Triticum turgidum TtNF-YA family members through genome-wide analysis. Twelve NF-YA genes were discovered in Triticum turgidum. Discovered genes were distributed across eight chromosomes, while their encoded proteins were localized in cell nucleus. Structure and motif pattern analyses revealed that the TtNF-YA genes were relatively conserved. The expression of TtNF-YAs genes was significantly induced by several stressors and their expression profiles differed in various tissues and at various development stages. Notably, TtNF-YA2 A-1 and TtNF-YA2B-1 exhibited the greatest increase in response to Polyethylene glycol, while TtNF-YA4 A and TtNF-YA4B-1 showed the highest increase under salt stress. Additionally, TtNF-YA5B-1 and TtNF-YA6 A-1 displayed pronounced upregulation when exposed to exogenous Abscisic acid, suggesting that TtNF-YA are involved in a series of cellular and developmental events. This finding was corroborated by the recognition of several cis-regulatory elements in the TtNF-YAs promoter region, associated with the applied treatments. Overexpression of TtNF-YA2 A-1, TtNF-YA2B-1, TtNF-YA4 A, TtNF-YA4 A-1, TtNF-YA4B-1, and TtNF-YA5 A-2 genes in Saccharomyces cerevisiae showed that these genes increase cell tolerance to multiple stresses. Our results will facilitate subsequent functional analysis of TtNF-YAs genes, which emerge as promising targets for genetic engineering for increasing wheat tolerance to multiple stresses.

Mining Genetic Variations Reveals the Differentiation of Gene Alternative Polyadenylation Involving in Rice Panicle Architecture Regulation

Panicle architecture is a critical determinant of rice yield and resilience, yet the genetic and environmental factors shaping this trait remain incompletely understood. Here, we applied an integrative genomic approach combining multi-locus association mapping, transcriptome analysis and population genomics to dissect the genetic basis of key panicle traits in rice. We identified robust genetic loci underlying the number of primary branches, panicle length and spikelets per panicle, with many showing sensitivity to temperature, underscoring the importance of gene-environment interactions for yield stability. Notably, we discovered that variation in alternative polyadenylation (APA) of specific transcripts is associated with panicle trait diversity at the population level, suggesting that regulatory mechanisms such as APA are significant contributors to phenotypic plasticity and adaptation. These findings deliver both novel candidate genes in panicle development and mechanistic insights to support the breeding of rice varieties with enhanced productivity and climate resilience.

Multi-Experiment and Multi-Locus Genome-Wide Association Mapping for Grain Arsenic in Rice Population

Rice is a globally important crop and is particularly efficient at assimilating arsenic (As). Identifying QTLs and genes associated with grain As is essential for breeding low-As rice cultivars. In this study, data on As accumulation in grains of Rice Diversity Panel 1 in five field environments at four diverse geographic sites were reanalyzed to compare genome-wide association (GWA) methods. Two single-locus (EMMAX for single trait and GEMMA for multi-experiments) and six multi-locus (FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM) GWA methods were used. A total of 90 and 111 QTLs were detected using EMMAX and GEMMA, respectively. A total of 2, 11, 12, 19, 23, and 25 QTNs were identified by FASTmrEMMA, ISIS EM-BLASSO, mrMLM, pKWmEB, pLARmEB, and FASTmrMLM, respectively. Among these, 22 QTLs/QTNs were co-detected by single-locus and multi-locus GWAS methods. From these QTLs/QTNs, a total of 10 candidate genes were identified. Analysis of the haplotype variants of one candidate genes, OsABCC1, and one cluster of the plasma membrane intrinsic proteins genes revealed that a greater than 10% reduction in grain As could be achieved. The QTLs/QTNs and candidate genes identified give insight into the molecular mechanisms regulating As accumulation in rice and serve as breeding targets for developing low grain As rice cultivars.

A pangenome reference of wild and cultivated rice

Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.

Large-scale genomic and phenomic analyses of modern cultivars empower future rice breeding design

Modern cultivated rice plays a pivotal role in global food security. China accounts for nearly 30% of the world's rice production and has developed numerous cultivated varieties over the past decades that are well adapted to diverse growing regions. However, the genomic bases underlying the phenotypes of these modern cultivars remain poorly characterized, limiting the exploitation of this vast resource for breeding specialized, regionally adapted cultivars. In this study, we constructed a comprehensive genetic variation map of modern rice using resequencing datasets from 6044 representative cultivars from five major rice-growing regions in China. Our genomic and phenotypic analyses of this diversity panel revealed regional preferences for specific genomic backgrounds and traits, such as heading date, biotic/abiotic stress resistance, and grain shape, which are crucial for adaptation to local conditions and consumer preferences. We identified 3131 quantitative trait loci associated with 53 phenotypes across 212 datasets under various environmental conditions through genome-wide association studies. Notably, we cloned and functionally verified a novel gene related to grain length, OsGL3.6. By integrating multiple datasets, we developed RiceAtlas, a versatile multi-scale toolkit for rice breeding design. We successfully utilized the RiceAtlas breeding design function to rapidly improve the grain shape of the Suigeng4 cultivar. These valuable resources enhance our understanding of the adaptability and breeding requirements of modern rice and can facilitate advances in future rice-breeding initiatives.

Genome-Wide Association Study and Candidate Gene Mining of Husk Number Trait in Maize

Husk number (HN) trait is an important factor affecting maize kernel dehydration rate after the physiological maturity stage. In general, a reasonable reduction in HN is a key target sought for breeding maize varieties that are suitable for mechanized harvesting. In this study, the HN of a maize natural population panel containing 232 inbred lines was analyzed, and the results showed a broad-sense heritability of 0.89, along with a wide range of phenotypic variation. With the best linear unbiased prediction (BLUP) values across the three environments, a genome-wide association study (GWAS) was conducted using 995,106 single-nucleotide polymorphism (SNP) markers. A total of 16 SNPs significantly associated with HN were identified by the mixed linear model and general linear model using the TASSEL 5.0 software program. A local linkage disequilibrium (LD) study was performed to infer the candidate interval around the lead SNPs. A total of 19 functionally annotated genes were identified. The candidate genes were divided into multiple functional types, including transcriptional regulation, signal transduction, and metabolic and cellular transport. These results provide hints for the understanding of the genetic basis of the HN trait and for the breeding of maize varieties with fewer HN and faster dehydration rate.

FZP modulates tillering via OsMADS57 in rice

The number of tillers in rice directly determines the number of panicles, which is crucial for enhancing plant architecture and achieving high yields. Some important genes regulating rice tillering have been identified, but their underlying mechanisms remain unclear. FRIZZY PANICLE (FZP) encodes an AP2/ERF transcription factor. Beyond its well-established role in promoting spikelet formation during the reproductive phase, here we demonstrate that FZP also inhibits axillary buds outgrowth in the vegetative phase by suppressing the expression of a MADS-box gene (OsMADS57) that functions as a growth promoter. Consequently, genome editing of the FZP-bound cis-motif in the promoter of OsMADS57 releases its expression, leading to more tillers. Furthermore, domestication analysis shows that FZP has undergone strong selection in cultivated rice, while the downstream gene OsMADS57 has been differentiated between indica and japonica subspecies. Four functional SNPs in the promoter of OsMADS57 can increase rice tillering in most indica accessions by enhancing its expression. Our findings expose hidden pleiotropy of classic spikelet identity genes that are redeployed to control stem form, potentially enriching the gene resources for rice genetic improvement.

Genome-wide profiling of polymorphic short tandem repeats and their influence on gene expression and trait variation in diverse rice populations

Short tandem repeats (STRs) modulate gene expression and contribute to trait variation. However, a systematic evaluation of the genomic characteristics of STRs has not been conducted, and their influence on gene expression in rice remains unclear. Here, we construct a map of 137,629 polymorphic STRs in the rice (Oryza sativa L.) genome using a population-scale resequencing dataset. A genome-wide survey encompassing 4726 accessions shows that the occurrence frequency, mutational patterns, chromosomal distribution, and functional properties of STRs are correlated with the sequences and lengths of repeat motifs. Leveraging a transcriptome dataset from 127 rice accessions, we identify 44,672 expression STRs (eSTRs) by modeling gene expression in response to the length variation of STRs. These eSTRs are notably enriched in the regulatory regions of genes with active transcriptional signatures. Population analysis identifies numerous STRs that have undergone genetic divergence among different rice groups and 1726 tagged STRs that may be associated with agronomic traits. By editing the (ACT)7 STR in OsFD1 promoter, we further experimentally validate its role in regulating gene expression and phenotype. Our study highlights the contribution of STRs to transcriptional regulation in plants and establishes the foundation for their potential use as alternative targets for genetic improvement.

Genetic dissection of flowering time and fine mapping of qFT.A02-1 in rapeseed (Brassica napus L.)

KEY MESSAGE

qFT.A02-1, a major quantitative trait locus controlling flowering time in Brassica napus, was mapped to a 104.8-kb region on chromosome A02, and BnaA02G0156900ZS is the candidate gene in response for flowering time. Flowering time is a key agronomic trait that determines the adaptability of crops to the environment and thus affects yields. The mechanism underlying flowering time is still far from clear in Brassica napus. In this study, a recombinant inbred line population composed of 215 lines was constructed and 35 flowering time QTLs were identified. One major QTL, qFT.A02-1 (explaining 16.40-17.80% of phenotypic variation), was detected in two environments, which was confirmed by QTL-seq. A residual heterozygous line containing qFT.A02-1 for flowering time was further constructed, and qFT.A02-1 was subsequently fine-mapped to a 104.8-kb interval, wherein a total of 11 genes were predicted. Candidate gene functional annotation implied that BnaA02G0156900ZS, a homologous gene of FLOWERING LOCUS T in B. napus, was likely the candidate gene for qFT.A02-1. HiFi sequencing of the two parents was subsequently conducted, and a 1,079-bp insertion in the promoter of BnaA02. FT was confirmed. The allelic variation analysis in a diversity of accessions identified another 6 SNPs existing in the non-coding region of BnaA02. FT and the 1,079-bp insertion in promoter region are closely associated with the flowering time in B. napus. Haplotype analysis indicated that the flowering time of Hap02 is significantly earlier than Hap01 and Hap04, and Hap05 is significantly earlier than Hap04. Yield-related trait analysis revealed that there are no significant differences in yield-related traits between the two near-isogenic lines based on the target locus. These results may advance our understanding of the mechanism underlying flowering time in B. napus.

Optimizing breeding strategies for early-maturing white maize through genetic diversity and population structure

Maize production and productivity in sub-Saharan Africa are constrained by various factors. Assessing the genetic diversity of newly developed elite inbred lines can help identify lines with desirable genes and explore genetic relatedness for heterotic breeding. The objectives of this study were to assess the level of genetic diversity, and population structure, and identify appropriate clustering methods for assigning maize inbreds into heterotic groups. Three hundred and seventy-six elite inbreds extracted from three source populations were genotyped using Diversity Array Technology (DArTtag) mid-density platform. Results from 1904 of 3,305 SNP marker obtained revealed average marker polymorphism information content (PIC) of 0.39, observed heterozygosity of 0.02, gene diversity of 0.37, minor allele frequency of 0.29, Shannon and Simpson indices of 6.86 and 949.09, respectively, and allele richness of 787.70. The optimum sub-population was three defined by an admixture-based model and principal component analysis. The average genetic distance was 0.303 varying from 0.03 (TZEI 2772 × TZEI 2761) to 0.372 (TZEI 2273 × TZEI 2832). For appropriate heterotic classification of the 376 elite inbreds, the use of IBS distance matrix and average linkage clustering method provided the highest cophenetic correlation coefficient (0.97). Three heterotic group (HG) were identified using IBS distance and average linkage clustering method with HG 1 have 188 inbreds, HG 2 having 137, and HG 3 having 59 inbreds. The pedigree-based phylogenetic tree showed substantial consistency with the heterotic groups identified. The F-statistics based on the underlying population structure revealed 10% variation among sub-populations and 90% variation within sub-populations with a moderate level of genetic differentiation (0.10). The elite inbred lines showed a high degree of genetic diversity, which could be beneficial for developing new, early-maturing white hybrids to mitigate production constraints in sub-Saharan Africa.

Genome-wide association study revealed candidate genes associated with leaf size in alfalfa (Medicago sativa L.)

BACKGROUND

Alfalfa (Medicago sativa L.) is one of the most widely cultivated perennial leguminous forages globally, known for its high yield and quality. Leaf size plays a crucial role in influencing its photosynthetic capacity, forage yield, and quality. Therefore, understanding the genetic factors regulating leaf size is of great importance for breeding new alfalfa varieties with improved yield and quality. In this study, we performed a genome-wide association study on four leaf size-related traits in 176 alfalfa germplasm resources to identify candidate genes associated with leaf size.

RESULTS

Phenotypic analysis revealed varying degrees of variation among the four traits, with coefficients of variation ranging from 3.43 to 36.84%. The broad sense heritability of these traits was found to be between 38.30% and 53.23%. Correlation analysis showed a significant positive correlation among the four traits (P < 0.01). The GWAS identified 39 SNPs associated with leaf size, distributed across eight chromosomes, of which 9 SNPs were linked to multiple traits. Haplotype analysis further confirmed that the number of superior alleles in each material was positively correlated with leaf area. Finally, we identified five genes near these 39 significant SNPs that are associated with leaf size or development.

CONCLUSION

Our findings provide new molecular markers for marker-assisted selection in alfalfa breeding programs. Moreover, this study provides a solid foundation for subsequent functional verification and genetic improvement in alfalfa.

Dissecting the Genetic Basis of Preharvest Sprouting in Rice Using a Genome-Wide Association Study

Preharvest sprouting (PHS) is an unfavorable trait in cereal crops that significantly reduces grain yield and quality. However, the regulatory mechanisms underlying this complex trait are still largely unknown. Here, 276 rice accessions from the 3000 Rice Genomes Project were used to perform a genome-wide association study. In total, seven PHS-associated quantitative trait loci (QTLs) were identified, including two novel QTLs and five previously reported QTLs. Among them, four QTLs were identified in 2020 and 2021, and rice accessions carrying at least two favorable alleles exhibited significantly improved PHS resistance. Within these four stable QTLs, five candidate genes were identified based on haplotype and gene expression analyses, including two genes in qPhs-1.1, one gene in qPhs-3, one gene in qPhs-6, and one gene in qPhs-7. Notably, the novel QTL qPhs-6 was found to contain the candidate gene Pi starvation-induced transcription factor 1 (OsPTF1). We discovered that OsPTF1 plays a novel role in negatively regulating PHS in rice and identified two elite haplotypes of OsPTF1 associated with low PHS. Our results provide future insight into the genetic basis of PHS and will prove useful in the future studies on the role of OsPTF1 in PHS in rice.

Mining genomic regions associated with stomatal traits and their candidate genes in bread wheat through genome-wide association study (GWAS)

KEY MESSAGE

112 candidate quantitative trait loci (QTLs) and 53 key candidate genes have been identified as associated with stomatal traits in wheat. These include bHLH, MADS-box transcription factors, and mitogen-activated protein kinases (MAPKs). Stomata is a common feature of the leaf surface of plants and serve as vital conduits for the exchange of gases (primarily CO₂ and water vapor) between plants and the external environment. In this study, a comprehensive genome analysis was conducted by integrating genome-wide association study (GWAS) and genome prediction to identify the genomic regions and candidate genes of stomatal traits associated with drought resistance and water-saving properties in a panel of 184 diverse bread wheat genotypes. There were significant variations on stomatal traits in the wheat panel across different environmental conditions. GWAS was conducted with the genotypic data from the wheat 660 K single-nucleotide polymorphism (SNP) chip, and the stomatal traits conducted across three environments during two growing seasons. The final GWAS identified 112 candidate QTLs that exhibited at least two significant marker-trait associations. Subsequent analysis identified 53 key candidate genes, including 13 bHLH transcription factor, 2 MADS-box transcription factors, and 4 mitogen-activated protein kinase genes, which may be strongly associated with stomatal traits. The application of Bayesian ridge regression for genomic prediction yielded an accuracy rate exceeding 60% for all four stomatal traits in both SNP matrices, with stomatal width achieving a rate in excess of 70%. Additionally, three Kompetitive allele-specific PCR markers were developed and validated, representing a significant advancement in marker-assisted prediction. Overall, these results will contribute to a more comprehensive understanding of wheat stomatal traits and provide a valuable reference for germplasm screening and innovation in wheat germplasm with novel stomatal traits.

Adverse effects of heat shock in rice (Oryza sativa L.) and approaches to mitigate it for sustainable rice production under the changing climate: A comprehensive review

Heat shock, a transient exposure to high temperatures, is a substantial hazard to rice (Oryza sativa L.) production and sustainability. The objective of this review paper is to summarize the impact of heat shock on rice and explore approaches to mitigate its adverse effects to achieve sustainable production. Rice is a staple food for billions of people globally and is extremely sensitive to heat shock. Higher temperatures disturb various physiological and biochemical processes, resulting in decreased growth, development, and ultimately lower grain yield. Heat shock negatively affects important agronomic traits, such as panicle differentiation, pollen viability, fertilization, grain filling, and, ultimately, grain quality. To manage heat shock and sustain rice production, several strategies have been explored, such as modifications to sowing schedules, the substitution of heat-tolerant cultivars for sensitive genotypes, and the use of growth regulators. To improve rice under heat shock, various approaches could be taken: (1) cultivating cultivars that flower early in the morning by adjusting sowing/planting times, modified irrigation, and fertilization; (2) inducing acclimation via growth regulators and organic stimulants and chemicals; (3) breeding genetically resistant cultivars through the integration of appropriate genes; and (4) genetic modification techniques for heat-shock tolerance. Overall, effectively managing heat-shock stress in rice requires a comprehensive strategy that includes developing and using heat shock-tolerant cultivars, adopting suitable cultural practices, utilizing external substances, and applying biotechnological tools. Implementing these strategies collectively will help achieve sustainable rice production in the face of increasing heat-shock conditions.

A genome-wide association study using Myanmar indica diversity panel reveals a significant genomic region associated with heading date in rice

Heading date is a key agronomic trait for adapting rice varieties to different growing areas and crop seasons. The genetic mechanism of heading date in Myanmar rice accessions was investigated using a genome-wide association study (GWAS) in a 250-variety indica diversity panel collected from different geographical regions. Using the days to heading data collected in 2019 and 2020, a major genomic region associated with the heading date, designated as MTA3, was found on chromosome 3. The linkage disequilibrium block of the MTA3 contained the coding sequence (CDS) of the phytochrome gene PhyC but not in its promoter region. Haplotype analysis of the 2-kb promoter and gene regions of PhyC revealed the six haplotypes, PHYCHapA, B, C, D, E, and F. The most prominent haplotypes, PHYCHapA and PHYCHapC, had different CDS and were associated with late heading and early heading phenotypes in MIDP, respectively. The difference in CDS effects between the PHYCHapB, which has identical CDS to PHYCHapA, and PHYCHapC was validated by QTL analysis using an F2 population. The distribution of PHYCHapA in the southern coastal and delta regions and of PHYCHapC in the northern highlands appears to ensure heading at the appropriate time in each area under the local day-length conditions in Myanmar. The natural variation in PhyC would be a major determinant of heading date in Myanmar accessions.

Genome-wide characterization of PEBP genes in Mung bean (Vigna radiata L.) with functional analysis of VrFT1 in relation to photoperiod

Mung bean (Vigna radiata L.), a widely cultivated legume, belongs to the Fabaceae family's Papilionoideae subfamily. Although Phosphatidylethanolamine-binding protein (PEBP) genes have been identified in several plant species, their presence and function in mung bean remain largely unexplored. In this study, we identified seven VrPEBP genes from mung bean and classified them into four clades: FT, MFT, TFL and FT-like. Cis-regulatory element analysis revealed that VrPEBP genes may play a role in light, hormone, and stress responses. Quantitative real-time PCR (qRT-PCR) analysis indicated that VrPEBPs were constitutively expressed in various tissues. However, tissue-specific expression patterns were observed among VrPEBP genes. Under short-day (SD) conditions, VrFT1 and VrMFT1 exhibited significantly higher expression levels than under long-day (LD) conditions at 8 and 4 h, respectively. Conversely, VrTFL2 and VrTFL3 showed significantly higher expression levels under LD conditions compared to SD conditions at 8 and 12 h, respectively. The varied expression patterns of these genes under different photoperiod suggest their potential involvement in the photoperiodic regulation of flowering in mung bean. Additionally, phenotypic analysis of transgenic Arabidopsis plants overexpressing VrFT1 revealed higher expression levels under SD conditions and predicted its role in promoting flowering. These results provide valuable insights into the evolution and function of PEBP genes in mung bean and lay the foundation for further research on their regulatory mechanisms and potential applications in mung bean improvement.

Genetic Diversity and Association Analysis of Traits Related to Water-Use Efficiency and Nitrogen-Use Efficiency of Populus deltoides Based on SSR Markers

Populus deltoides is one of the primary tree species for bioenergy production in temperate regions. In arid/semi-arid northern China, the scarcity of water and nitrogen significantly limits the productivity of poplar plantations. The identification of relevant molecular markers can promote the breeding of resource-efficient varieties. In this study, 188 genotypes of P. deltoides from six provenances served as experimental material. Genetic differentiation analysis, analysis of molecular variance (AMOVA), principal coordinate analysis (PCoA), unweighted pair group method with arithmetic mean (UPGMA) clustering, and genetic structure analysis were performed using selected simple sequence repeat (SSR) markers. Based on these analyses, the association analysis of water-use efficiency (WUE) and nitrogen-use efficiency (NUE) were conducted using general linear model (GLM) and mixed linear model (MLM) approaches. The results showed that 15 pairs of SSR primers successfully amplified across all 188 individuals, with an average of 7.33 alleles (Na) observed per primer pair. The polymorphism information content (PIC) ranged from 0.060 to 0.897, with an average of 0.544, indicating high genetic diversity in the selected markers. The average inbreeding coefficient intra-population (Fis), inbreeding coefficient inter-population (Fit), and inter-population genetic fraction coefficient (Fst) values were 0.005, 0.135, and 0.132, respectively, indicating high heterozygosity, substantial inbreeding within populations, and moderate genetic differentiation, with an average gene flow (Nm) of 1.964, suggesting substantial gene flow between populations. Additionally, molecular variance was primarily within individuals (84.12%). Genetic structure analysis revealed four subgroups, with some degree of genetic admixture among the provenances. In the GLM model, 11 markers were significantly associated with five traits (p < 0.05), with an average contribution rate of 15.82%. Notably, SSR132 and SSR143 were significantly associated with multiple traits (p < 0.05). The MLM model identified two markers (SSR47 and SSR85) significantly associated with ground diameter (p < 0.05) and one marker (SSR80) significantly associated with NUE (p < 0.05). This study identifies loci associated with WUE and NUE, laying a foundation for future genetic improvement and marker-assisted breeding strategies in poplar.

Extreme-Phenotype Genome-Wide Association Analysis for Growth Traits in Spotted Sea Bass (Lateolabrax maculatus) Using Whole-Genome Resequencing

Spotted sea bass (Lateolabrax maculatus) is an important marine economic fish in China, ranking third in annual production among marine fish. However, a declined growth rate caused by germplasm degradation has severely increased production costs and reduced economic benefits. There is an urgent need to develop the fast-growing varieties of L. maculatus and elucidate the genetic mechanisms underlying growth traits. Here, whole-genome resequencing technology combined with extreme phenotype genome-wide association analysis (XP-GWAS) was used to identify candidate markers and genes associated with growth traits in L. maculatus. Two groups of L. maculatus, consisting of 100 fast-growing and 100 slow-growing individuals with significant differences in body weight, body length, and carcass weight, underwent whole-genome resequencing. A total of 4,528,936 high-quality single nucleotide polymorphisms (SNPs) were used for XP-GWAS. These SNPs were evenly distributed across all chromosomes without large gaps, and the average distance between SNPs was only 175.8 bp. XP-GWAS based on the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (Blink) and Fixed and random model Circulating Probability Unification (FarmCPU) identified 50 growth-related markers, of which 17 were related to body length, 19 to body weight, and 23 to carcass weight. The highest phenotypic variance explained (PVE) reached 15.82%. Furthermore, significant differences were observed in body weight, body length, and carcass weight among individuals with different genotypes. For example, there were highly significant differences in body weight among individuals with different genotypes for four SNPs located on chromosome 16: chr16:13133726, chr16:13209537, chr16:14468078, and chr16:18537358. Additionally, 47 growth-associated genes were annotated. These genes are mainly related to the metabolism of energy, glucose, and lipids and the development of musculoskeletal and nervous systems, which may regulate the growth of L. maculatus. Our study identified growth-related markers and candidate genes, which will help to develop the fast-growing varieties of L. maculatus through marker-assisted breeding and elucidate the genetic mechanisms underlying the growth traits.

Cellulose synthase-like OsCSLD4: a key regulator of agronomic traits, disease resistance, and metabolic indices in rice

KEY MESSAGE

Cellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.

A KNOX Ⅱ transcription factor suppresses the NLR immune receptor BRG8-mediated immunity in rice

Nucleotide-binding site and leucine-rich repeat (NLR) proteins are activated by detecting pathogen effectors, which in turn trigger host defenses and cell death. Although many NLRs have been identified, the mechanisms responsible for NLR-triggered defense responses are still poorly understood. In this study, through a genome-wide association study approach, we identified a novel NLR gene, Blast Resistance Gene 8 (BRG8), which confers resistance to rice blast and bacterial blight diseases. BRG8 overexpression and complementation lines exhibit enhanced resistance to both pathogens. Subcellular localization assays showed that BRG8 is localized in both the cytoplasm and the nucleus. Additional evidence revealed that nuclear-localized BRG8 can enhance rice immunity without a hypersensitive response (HR)-like phenotype. We also demonstrated that the coiled-coil domain of BRG8 not only physically interacts with itself but also interacts with the KNOX Ⅱ protein HOMEOBOX ORYZA SATIVA59 (HOS59). Knockout mutants of HOS59 in the BRG8 background show enhanced resistance to Magnaporthe oryzae strain CH171 and Xoo strain CR4, similar to that of the BRG8 background. By contrast, overexpression of HOS59 in the BRG8 background will compromise the HR-like phenotype and resistance response. Further analysis revealed that HOS59 promotes the degradation of BRG8 via the 26S proteasome pathway. Collectively, our study highlights HOS59 as an NLR immune regulator that fine-tunes BRG8-mediated immune responses against pathogens, providing new insights into NLR associations and functions in plant immunity.

Genome-wide association study identifies the genetic basis of key agronomic traits in 207 sugar beet accessions

Sugar beet (Beta vulgaris) has emerged as one of the two primary crops, alongside sugarcane, for global sugar production. Comprehensively understanding sucrose synthesis, transport, and accumulation in sugar beet holds great significance for enhancing sugar production. In this study, we collected a diverse set of 269 sugar beet accessions worldwide and measured 12 phenotypes, comprising biomass, soluble sugar content, and 10 taproot-related traits. We re-sequenced 207 accessions to explore genetic diversity and population structure. Then we employed a genome-wide association study (GWAS) and RNA-seq to identify single-nucleotide polymorphisms and genes associated with natural phenotypic variations. Our findings revealed a panel of genes potentially regulating biomass and sugar accumulation, notably the dual-role gene UDP-glucose 4-epimerase, which genetically balances sugar accumulation and cell wall synthesis. In summary, this study provides a foundation for molecular breeding in sugar beet.

Modern Plant Breeding Techniques in Crop Improvement and Genetic Diversity: From Molecular Markers and Gene Editing to Artificial Intelligence-A Critical Review

With the development of new technologies in recent years, researchers have made significant progress in crop breeding. Modern breeding differs from traditional breeding because of great changes in technical means and breeding concepts. Whereas traditional breeding initially focused on high yields, modern breeding focuses on breeding orientations based on different crops' audiences or by-products. The process of modern breeding starts from the creation of material populations, which can be constructed by natural mutagenesis, chemical mutagenesis, physical mutagenesis transfer DNA (T-DNA), Tos17 (endogenous retrotransposon), etc. Then, gene function can be mined through QTL mapping, Bulked-segregant analysis (BSA), Genome-wide association studies (GWASs), RNA interference (RNAi), and gene editing. Then, at the transcriptional, post-transcriptional, and translational levels, the functions of genes are described in terms of post-translational aspects. This article mainly discusses the application of the above modern scientific and technological methods of breeding and the advantages and limitations of crop breeding and diversity. In particular, the development of gene editing technology has contributed to modern breeding research.

Streamlined whole-genome genotyping through NGS-enhanced thermal asymmetric interlaced (TAIL)-PCR

Whole-genome genotyping (WGG) stands as a pivotal element in genomic-assisted plant breeding. Nevertheless, sequencing-based approaches for WGG continue to be costly, primarily owing to the high expenses associated with library preparation and the laborious protocol. During prior development of foreground and background integrated genotyping by sequencing (FBI-seq), we discovered that any sequence-specific primer (SP) inherently possesses the capability to amplify a massive array of stable and reproducible non-specific PCR products across the genome. Here, we further improved FBI-seq by replacing the adapter ligated by Tn5 transposase with an arbitrary degenerate (AD) primer. The protocol for the enhanced FBI-seq unexpectedly mirrors a simplified thermal asymmetric interlaced (TAIL)-PCR, a technique that is widely used for isolation of flanking sequences. However, the improved TAIL-PCR maximizes the primer-template mismatched annealing capabilities of both SP and AD primers. In addition, leveraging of next-generation sequencing enhances the ability of this technique to assay tens of thousands of genome-wide loci for any species. This cost-effective, user-friendly, and powerful WGG tool, which we have named TAIL-PCR by sequencing (TAIL-peq), holds great potential for widespread application in breeding programs, thereby facilitating genome-assisted crop improvement.

Characterization of quantitative trait loci from DJ123 (aus) independently affecting panicle structure traits in indica rice cultivar IR64

The rice panicle is the principal organ to influence productivity and traits affecting panicle architecture determine sink size and yield potential. Improving panicle architecture may be effective in increasing yield under low-input conditions, but which traits are of importance under such conditions and how they are genetically controlled is not well understood. Using recombinant inbred lines (RILs) derived from a cross between a modern variety IR64 and a low fertility tolerant accession DJ123, quantitative trait locus (QTL) mapping was conducted under high soil fertility in Japan and low fertility in Madagascar. Among QTL for panicle length (PL) detected, the DJ123 allele increased rachis length at qCL1 and qPL9, while the IR64 allele increased primary branch length at qPL7. DJ123 further contributed two QTL for grain width whereas IR64 contributed two grain length QTL. Analysis of lines carrying different combinations of detected QTL indicates that rachis and primary branch lengths are independently regulated, explaining strong transgressive segregation for PL. The positive effects of PL-related QTL were further confirmed by a genome-wide analysis of allelic states in two breeding lines that had been selected repeatedly for total panicle weight per plant under low input conditions. This study provides the genetic basis for complex panicle architecture in rice and will aid in designing an ideal panicle architecture that leads to increased yield under low fertility conditions.

Supplementary information

The online version contains supplementary material available at 10.1007/s11032-024-01494-5.

Dissecting the genetic basis of UV-B responsive metabolites in rice

BACKGROUND

UV-B, an important environmental factor, has been shown to affect the yield and quality of rice (Oryza sativa) worldwide. However, the molecular mechanisms underlying the response to UV-B stress remain elusive in rice.

RESULTS

We perform comprehensive metabolic profiling of leaves from 160 diverse rice accessions under UV-B and normal light conditions using a widely targeted metabolomics approach. Our results reveal substantial differences in metabolite accumulation between the two major rice subspecies indica and japonica, especially after UV-B treatment, implying the possible role and mechanism of metabolome changes in subspecies differentiation and the stress response. We next conduct a transcriptome analysis from four representative rice varieties under UV-B stress, revealing genes from amino acid and flavonoid pathways involved in the UV-B response. We further perform a metabolite-based genome-wide association study (mGWAS), which reveals 3307 distinct loci under UV-B stress. Identification and functional validation of candidate genes show that OsMYB44 regulates tryptamine accumulation to mediate UV-B tolerance, while OsUVR8 interacts with OsMYB110 to promote flavonoid accumulation and UV-B tolerance in a coordinated manner. Additionally, haplotype analysis suggests that natural variation of OsUVR8groupA contributes to UV-B resistance in rice.

CONCLUSIONS

Our study reveals the complex biochemical and genetic foundations that govern the metabolite dynamics underlying the response, tolerance, and adaptive strategies of rice to UV-B stress. These findings provide new insights into the biochemical and genetic basis of the metabolome underlying the crop response, tolerance, and adaptation to UV-B stress.

Overexpression of Orysa;KRP4 drastically reduces grain filling in rice

MAIN CONCLUSION

Excess of KRP4 in the developing kernels in rice causes poor filling of the grains possibly through inhibition of CDKA;2 and CDKB;1 activity mediated by its interaction with CDKF;3. The potential yield of the rice varieties producing compact and heavy panicles bearing numerous spikelets is compromised because a high percentage of spikelets remain poorly filled, reportedly because of a high expression of KRPs that causes suppression of endosperm cell proliferation. To test the stated negative relationship between KRP expression and grain filling, Orysa;KRP4 was overexpressed under the control of seed-specific glutelin promoter in IR-64 rice variety that shows good grain filling. The transgenic lines showed more than 15-fold increase in expression of KRP4 in the spikelets concomitant with nearly 50% reduction in grain filling compared with the wild type without producing any significant changes on the other yield-related parameters like panicle length and the spikelets numbers that were respectively 30.23 ± 0.89 cm and 229.25 ± 33.72 per panicle in the wild type, suggesting a highly organ-targeted effect of the genetic transformation. Yeast two-hybrid test revealed CDKF;3 as the interacting partner of KRP4, and CDKF;3 was found to interact with CDKA;2, CDKB;1 and CDKD;1. Significant decrease in grain filling in the transgenic lines compared with the wild type due to overexpression of KRP4 could be because of suppression of the activity of CDKB;1 and CDKA;2 by inhibition of their phosphorylation directly by CDKF;3, or mediated through inhibition of phosphorylation of CDKD;1 by CDKF;3. The study thus indicated that suppression of expression of KRP(s) by genetic manipulation of their promoters could be an important way of improving the yield of the rice varieties bearing compact and heavy panicles.

Improving Rice Quality by Regulating the Heading Dates of Rice Varieties without Yield Penalties

The heading date, a critical trait influencing the rice yield and quality, has always been a hot topic in breeding research. Appropriately delaying the flowering time of excellent northern rice varieties is of great significance for improving yields and enhancing regional adaptability during the process for introducing varieties from north to south. In this study, genes influencing the heading date were identified through genome-wide association studies (GWAS). Using KenDao 12 (K12), an excellent cultivar from northern China, as the material, the specific flowering activator, OsMADS50, was edited using the genome-editing method to regulate the heading date to adapt to the southern planting environment. The results indicated that the osmads50 mutant line of K12 flowered about a week later, with a slight increase in the yield and good adaptability in the southern region in China. Additionally, the expressions of key flowering regulatory genes, such as Hd1, Ghd7, Ehd1, Hd3a, and RFT1, were reduced in the mutant plants, corroborating the delayed flowering phenotype. Yield trait analysis revealed that the primary factor for improved yield was an increase in the number of effective tillers, although there is potential for further enhancements in the seed-setting rate and grain plumpness. Furthermore, there were significant increases in the length-to-width ratio of the rice grains, fat content, and seed transparency, all contributing to an overall improvement in the rice quality. In summary, this study successfully obtained a rice variety with a delayed growth period through OsMADS50 gene editing, effectively implementing the strategy for adapting northern rice varieties to southern climates. This achievement significantly supports efforts to enhance the rice yield and quality as well as to optimize production management practices.

Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date

The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of quantitative trait locus (QTL) mapping, but single nucleotide polymorphism (SNP)-based GWAS does not fully reach its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice. A total of 44 000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24 414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of <55 kb for major effect genes and <123 kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding.

Transcriptome-referenced association study provides insights into the regulation of oil and fatty acid biosynthesis in Torreya grandis kernel

INTRODUCTION

Torreya grandis is a gymnosperm belonging to Taxodiaceae. As an economically important tree, its kernels are edible and rich in oil with high unsaturated fatty acids, such as sciadonic acid. However, the kernels from different T. grandis landraces exhibit fatty acid and oil content variations.

OBJECTIVES

As a gymnosperm, does T. grandis have special regulation mechanisms for oil biosynthesis? The aim of this study was to dissect the genetic architecture of fatty acid and oil content and the underlying mechanism in T. grandis.

METHODS

We constructed a high integrity reference sequence of expressed regions of the genome in T. grandis and performed transcriptome-referenced association study (TRAS) for 10 fatty acid and oil traits of kernels in the 170 diverse T. grandis landraces. To confirm the TRAS result, we performed functional validation and molecular biology experiments for oil significantly associated genes.

RESULTS

We identified 41 SNPs from 34 transcripts significantly associated with 7 traits by TRAS (-log10 (P) greater than 6.0). Results showed that LOB domain-containing protein 40 (LBD40) and surfeit locus protein 1 (SURF1) may be indirectly involved in the regulation of oil and sciadonic acid biosynthesis, respectively. Moreover, overexpression of TgLBD40 significantly increased seed oil content. The nonsynonymous variant in the TgLBD40 coding region discovered by TRAS could alter the oil content in plants. Pearson's correlation analysis and dual-luciferase assay indicated that TgLBD40 positively enhanced oil accumulation by affecting oil biosynthesis pathway genes, such as TgDGAT1.

CONCLUSION

Our study provides new insights into the genetic basis of oil biosynthesis in T. grandis and demonstrates that integrating RNA sequencing and TRAS is a powerful strategy to perform association study independent of a reference genome for dissecting important traits in T. grandis.

Genomic investigation of 18,421 lines reveals the genetic architecture of rice

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.

Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh

Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

Quantitative Trait Locus Mapping for Plant Height and Branch Number in CCRI70 Recombinant Inbred Line Population of Upland Cotton (Gossypium hirsutum)

Upland cotton accounts for a high percentage (95%) of the world's cotton production. Plant height (PH) and branch number (BN) are two important agronomic traits that have an impact on improving the level of cotton mechanical harvesting and cotton yield. In this research, a recombinant inbred line (RIL) population with 250 lines developed from the variety CCRI70 was used for constructing a high-density genetic map and identification of quantitative trait locus (QTL). The results showed that the map harbored 8298 single nucleotide polymorphism (SNP) markers, spanning a total distance of 4876.70 centimorgans (cMs). A total of 69 QTLs for PH (9 stable) and 63 for BN (11 stable) were identified and only one for PH was reported in previous studies. The QTLs for PH and BN harbored 495 and 446 genes, respectively. Combining the annotation information, expression patterns and previous studies of these genes, six genes could be considered as potential candidate genes for PH and BN. The results could be helpful for cotton researchers to better understand the genetic mechanism of PH and BN development, as well as provide valuable genetic resources for cotton breeders to manipulate cotton plant architecture to meet future demands.

GWAS analysis reveals the genetic basis of blast resistance associated with heading date in rice

Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.

Construction of a high-density genetic map based on large-scale marker development in Coix lacryma-jobi L. using specific-locus amplified fragment sequencing (slaf-seq)

Coix lacryma-jobi L. is one of the most economically and medicinally important corns. This study constructed a high-density genetic linkage map of C. lacryma-jobi based on a cross between the parents 'Qianyi No. 2' × 'Wenyi No. 2' and their F2 progeny through high-throughput sequencing and the construction of a specific-locus amplified fragment (SLAF) library. After pre-processing, 325.49 GB of raw data containing 1628 M reads were obtained. A total of 22,944 high-quality SLAFs were identified, among which 3952 SLAFs and 3646 polymorphic markers met the requirements for the construction of a genetic linkage map. The integrated map contained 3605 high-quality SLAFs, which were grouped into ten genetic linkage groups. The total length of the map was 1620.39 cM, with an average distance of 0.45 cM and an average of 360.5 markers per linkage group. This report presents the first high-density genetic map of C. lacryma-jobi. This map was constructed using an F2 population and SLAF-seq approach, which allows the development of a large number of polymorphic markers in a short period. These results provide a platform for precise gene/quantitative trait locus (QTL) mapping, map-based gene separation, and molecular breeding in C. lacryma-jobi. They also help identify a target gene for tracking, splitting quantitative traits, and estimating the phenotypic effects of each QTL for QTL mapping. They are of great significance for improving the efficiency of discovering and utilizing excellent gene resources of C. lacryma-jobi.

Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice

Pigmented rice stands out for its nutritional value and is gaining more and more attention. Wild rice, domesticated red rice, and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype. We performed population genetic analyses using 5104 worldwide rice accessions, including 2794 accessions with red or black pericarps, 85 of which were newly sequenced in this study. The results suggested an evolutionary trajectory of red landraces originating from wild rice, and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years. Cultivated red rice was found to feralize to weedy rice, and weedy rice could be further re-domesticated to cultivated red rice. A genome-wide association study based on the 2794 accessions with pigmented pericarps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization. Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.

A systematic review of ginsenoside biosynthesis, spatiotemporal distribution, and response to biotic and abiotic factors in American ginseng

American ginseng (Panax quinquefolius) has gained recognition as a medicinal and functional food homologous product with several pharmaceutical, nutritional, and industrial applications. However, the key regulators involved in ginsenoside biosynthesis, the spatiotemporal distribution characteristics of ginsenosides, and factors influencing ginsenosides are largely unknown, which make it challenging to enhance the quality and chemical extraction processes of the cultivated American ginseng. This review presents an overview of the pharmacological effects, biosynthesis and spatiotemporal distribution of ginsenosides, with emphasis on the impacts of biotic and abiotic factors on ginsenosides in American ginseng. Modern pharmacological studies have demonstrated that American ginseng has neuroprotective, cardioprotective, antitumor, antidiabetic, and anti-obesity effects. Additionally, most genes involved in the upregulation of ginsenoside biosynthesis have been identified, while downstream regulators (OSCs, CYP450, and UGTs) require further investigation. Futhermore, limited knowledge exists regarding the molecular mechanisms of the impact of biotic and abiotic factors on ginsenosides. Notably, the nonmedicinal parts of American ginseng, particularly its flowers, fibrous roots, and leaves, exhibit higher ginsenoside content than its main roots and account for a considerable amount of weight in the whole plant, representing promising resources for ginsenosides. Herein, the prospects of molecular breeding and metabolic engineering based on multi-omics to improve the unstable quality of cultivated American ginseng and the shortage of ginsenosides are proposed. This review highlights the gaps in the current research on American ginseng and proposes solutions to address these limitations, providing a guide for future investigations into American ginseng ginsenosides.

Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome

Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.

Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel

Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.

Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice

In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.

A SLAF-based high-density genetic map construction and genetic architecture of thermotolerant traits in maize (Zea mays L.)

The leaf scorching trait at flowering is a crucial thermosensitive phenotype in maize under high temperature stress (HS), yet the genetic basis of this trait remains poorly understood. In this study, we genotyped a 254 RIL-F2:8 population, derived from the leaf scorch-free parental inbred line Abe2 and the leaf scorching maternal inbred line B73, using the specific-locus amplified fragment sequencing (SLAF-seq) method. A total of 10,112 polymorphic SLAF markers were developed, and a high-density genetic map with a total length of 1,475.88 cM was constructed. The average sequencing depth of the parents was 55.23X, and that of the progeny was 12.53X. Then, we identified a total of 16 QTLs associated with thermotolerant traits at flowering, of which four QTLs of leaf scorching damage (LS) were distributed on chromosomes 1 (qLS1), 2 (qLS2.1, qLS2.2) and 3 (qLS3), which could explain 19.73% of phenotypic variation. Combining one qLS1 locus with QTL-seq results led to the identification of 6 candidate genes. Expression experiments and sequence variation indicated that Zm00001d033328, encoding N-acetyl-gamma-glutamyl-phosphate reductase, was the most likely candidate gene controlling thermotolerant traits at flowering. In summary, the high-density genetic map and genetic basis of thermotolerant traits lay a critical foundation for mapping other complex traits and identifying the genes associated with thermotolerant traits in maize.

Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice

Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.

QTL epistasis plays a role of homeostasis on heading date in rice

If there was no gene interaction, the gene aggregation effect would increase infinitely with the increase of gene number. Epistasis avoids the endless accumulation of gene effects, playing a role of homeostasis. To confirm the role, QTL epistases were analyzed by four single-segment substitution lines with heading date QTLs in this paper. We found that QTLs of three positive effects and one negative effect generated 62.5% negative dual QTL epistatic effects and 57.7% positive triple QTL epistatic effects, forming the relationship "positive QTLs-negative one order interactions-positive two order interactions". In this way, the aggregation effect of QTLs was partially neutralized by the opposite epistatic effect sum. There also were two exceptions, QTL OsMADS50 and gene Hd3a-2 were always with consistent effect directions with their epistases, implying they could be employed in pyramiding breeding with different objectives. This study elucidated the mechanism of epistatic interactions among four QTLs and provided valuable genetic resources for improving heading date in rice.

Identification and Analysis of Candidate Genes Associated with Yield Structure Traits and Maize Yield Using Next-Generation Sequencing Technology

The main challenge of agriculture in the 21st century is the continuous increase in food production. In addition to ensuring food security, the goal of modern agriculture is the continued development and production of plant-derived biomaterials. Conventional plant breeding methods do not allow breeders to achieve satisfactory results in obtaining new varieties in a short time. Currently, advanced molecular biology tools play a significant role worldwide, markedly contributing to biological progress. The aim of this study was to identify new markers linked to candidate genes determining grain yield. Next-generation sequencing, gene association, and physical mapping were used to identify markers. An additional goal was to also optimize diagnostic procedures to identify molecular markers on reference materials. As a result of the conducted research, 19 SNP markers significantly associated with yield structure traits in maize were identified. Five of these markers (28629, 28625, 28640, 28649, and 29294) are located within genes that can be considered candidate genes associated with yield traits. For two markers (28639 and 29294), different amplification products were obtained on the electrophorograms. For marker 28629, a specific product of 189 bp was observed for genotypes 1, 4, and 10. For marker 29294, a specific product of 189 bp was observed for genotypes 1 and 10. Both markers can be used for the preliminary selection of well-yielding genotypes.

Genome-wide association study reveals loci and candidate genes of flowering time in jute (Corchorus L.)

Suitable flowering time can improve fiber yield and quality, which is of great significance for jute biological breeding. In this study, 242 jute accessions were planted in Fujian for 2 consecutive years, and 244,593 SNPs distributed in jute genome were used for genome-wide association analysis of flowering time. A total of 19 candidate intervals (P < 0.0001) were identified by using GLM and FaST-LMM and were significantly associated with flowering time, with phenotypic variation explained (PVE) ranging from 5.8 to 18.61%. Six stable intervals that were repeatedly detected in different environments were further identified by the linkage disequilibrium heatmap. The most likely 7 candidate genes involved to flowering time were further predicted according to the gene functional annotations. Notably, functional analysis of the candidate gene CcPRR7 of the major loci qFT-3-1, a key factor in circadian rhythm in the photoperiodic pathway, was evaluated by linkage, haplotype, and transgenic analysis. β-glucuronidase (GUS) and luciferase (LUC) activity assay of the promoters with two specific haplotypes confirmed that the flowering time can be controlled by regulating the expression of CcPRR7. The model of CcPRR7 involved in the photoperiod regulation pathway under different photoperiods was proposed. These findings provide insights into genetic loci and genes for molecular marker-assisted selection in jute and valuable information for genetically engineering PRR7 homologs in plants.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01435-8.

Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize (Zea maize L.) through a Genome-Wide Association Study

Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.

Transcriptome-wide association analyses reveal the impact of regulatory variants on rice panicle architecture and causal gene regulatory networks

Panicle architecture is a key determinant of rice grain yield and is mainly determined at the 1-2 mm young panicle stage. Here, we investigated the transcriptome of the 1-2 mm young panicles from 275 rice varieties and identified thousands of genes whose expression levels were associated with panicle traits. Multimodel association studies suggested that many small-effect genetic loci determine spikelet per panicle (SPP) by regulating the expression of genes associated with panicle traits. We found that alleles at cis-expression quantitative trait loci of SPP-associated genes underwent positive selection, with a strong preference for alleles increasing SPP. We further developed a method that integrates the associations of cis- and trans-expression components of genes with traits to identify causal genes at even small-effect loci and construct regulatory networks. We identified 36 putative causal genes of SPP, including SDT (MIR156j) and OsMADS17, and inferred that OsMADS17 regulates SDT expression, which was experimentally validated. Our study reveals the impact of regulatory variants on rice panicle architecture and provides new insights into the gene regulatory networks of panicle traits.