Major Quantitative Trait Loci Research Articles

Selective allele stacking of a novel quantitative trait locus facilitates the enhancement of seed epicatechin content in soybean (Glycine max (L.) Merr.)

(-)-Epicatechin (EC), a primary form of flavan-3ol and a building block of proanthocyanidins, has health benefits as it is a potent antioxidant. So far, no quantitative trait loci (QTLs) associated with EC have yet been identified in soybean. In this study, QTLs for EC and hilum color were identified in recombinant inbred lines (RILs) derived from the varieties Jinpung and IT109098 using high-resolution single nucleotide polymorphism linkage mapping. This revealed two major QTLs for EC content, qEC06 and qEC08. qEC06 spanned the Tawny (T) locus encoding flavonoid 3′-hydroxylase. qEC08, located near the Inhibitor (I) locus on Chr08, was also a major QTL for hilum color; however, allelic stacking of qEC08 and I revealed no relationship between I and EC content. RILs with IT109098 alleles at both qEC06 and qEC08 had higher EC content than other lines. These results will enable the production of soybean varieties with high EC content via marker-assisted selection.

Understanding genome structure facilitates the use of wild lentil germplasm for breeding: A case study with shattering loci.

Plant breeders are generally reluctant to cross elite crop cultivars with their wild relatives to introgress novel desirable traits due to associated negative traits such as pod shattering. This results in a genetic bottleneck that could be reduced through better understanding of the genomic locations of the gene(s) controlling this trait. We integrated information on parental genomes, pod shattering data from multiple environments, and high-density genetic linkage maps to identify pod shattering quantitative trait loci (QTLs) in three lentil interspecific recombinant inbred line populations. The broad-sense heritability on a multi-environment basis varied from 0.46 (in LR-70, Lens culinaris × Lens odemensis) to 0.77 (in LR-68, Lens orientalis × L. culinaris). Genetic linkage maps of the interspecific populations revealed reciprocal translocations of chromosomal segments that differed among the populations, and which were associated with reduced recombination. LR-68 had a 2-5 translocation, LR-70 had 1-5, 2-6, and 2-7 translocations, and LR-86 had a 2-7 translocation in one parent relative to the other. Segregation distortion was also observed for clusters of single nucleotide polymorphisms on multiple chromosomes per population, further affecting introgression. Two major QTL, on chromosomes 4 and 7, were repeatedly detected in the three populations and contain several candidate genes. These findings will be of significant value for lentil breeders to strategically access novel superior alleles while minimizing the genetic impact of pod shattering from wild parents.

An orchestrated ethylene-gibberellin signaling cascade contributes to mesocotyl elongation and emergence of rice direct seeding.

A mechanized direct seeding of rice with less labor and water usage, has been widely adopted. However, this approach requires varieties that exhibit uniform seedling emergence. Mesocotyl elongation (ME) offers the main drive of fast emergence of rice seedlings from soils; nevertheless, its genetic basis remains unknown. Here, we identify a major rice quantitative trait locus Mesocotyl Elongation1 (qME1), an allele of the Green Revolution gene Semi-Dwarf1 (SD1), encoding GA20-oxidase for gibberellin (GA) biosynthesis. ME1 expression is strongly induced by soil depth and ethylene. When rice grains are direct-seeded in soils, the ethylene core signaling factor OsEIL1 directly promotes ME1 transcription, accelerating bioactive GA biosynthesis. The GAs further degrade the DELLA protein SLENDER RICE 1 (SLR1), alleviating its inhibition of rice PHYTOCHROME-INTERACTING FACTOR-LIKE13 (OsPIL13) to activate the downstream expansion gene OsEXPA4 and ultimately promote rice seedling ME and emergence. The ancient traits of long mesocotyl and strong emergence ability in wild rice and landrace were gradually lost in company with the Green Revolution dwarf breeding process, and an elite ME1-R allele (D349H) is found in some modern Geng varieties (long mesocotyl lengths) in northern China, which can be used in the direct seeding and dwarf breeding of Geng varieties. Furthermore, the ectopic and high expression of ME1 driven by mesocotyl-specific promoters resulted in rice plants that could be direct-seeded without obvious plant architecture or yield penalties. Collectively, we reveal the molecular mechanism of rice ME, and provide useful information for breeding new Green Revolution varieties with long mesocotyl suitable for direct-seeding practice.

Complex genetic architecture of the chicken Growth1 QTL region.

The genetic complexity of polygenic traits represents a captivating and intricate facet of biological inheritance. Unlike Mendelian traits controlled by a single gene, polygenic traits are influenced by multiple genetic loci, each exerting a modest effect on the trait. This cumulative impact of numerous genes, interactions among them, environmental factors, and epigenetic modifications results in a multifaceted architecture of genetic contributions to complex traits. Given the well-characterized genome, diverse traits, and range of genetic resources, chicken (Gallus gallus) was employed as a model organism to dissect the intricate genetic makeup of a previously identified major Quantitative Trait Loci (QTL) for body weight on chromosome 1. A multigenerational advanced intercross line (AIL) of 3215 chickens whose genomes had been sequenced to an average of 0.4x was analyzed using genome-wide association study (GWAS) and variance-heterogeneity GWAS (vGWAS) to identify markers associated with 8-week body weight. Additionally, epistatic interactions were studied using the natural and orthogonal interaction (NOIA) model. Six genetic modules, two from GWAS and four from vGWAS, were strongly associated with the studied trait. We found evidence of both additive- and non-additive interactions between these modules and constructed a putative local epistasis network for the region. Our screens for functional alleles revealed a missense variant in the gene ribonuclease H2 subunit B (RNASEH2B), which has previously been associated with growth-related traits in chickens and Darwin's finches. In addition, one of the most strongly associated SNPs identified is located in a non-coding region upstream of the long non-coding RNA, ENSGALG00000053256, previously suggested as a candidate gene for regulating chicken body weight. By studying large numbers of individuals from a family material using approaches to capture both additive and non-additive effects, this study advances our understanding of genetic complexities in a highly polygenic trait and has practical implications for poultry breeding and agriculture.

Fine-mapping and validation of the major quantitative trait locus QFlANG-4B for flag leaf angle in wheat.

This study precisely mapped and validated a quantitative trait locus (QTL) located on chromosome 4B for flag leaf angle in wheat. Flag leaf angle (FLANG) is closely related to crop architecture and yield. We previously identified the quantitative trait locus (QTL) QFLANG-4B for FLANG on chromosome 4B, located within a 14-cM interval flanked by the markers Xbarc20 and Xzyh357, using a mapping population of recombinant inbred lines (RILs) derived from a cross between Nongda3331 (ND3331) and Zang1817. In this study, we fine-mapped QFLANG-4B and validated its associated genetic effect. We developed a BC3F3 population using ND3331 as the recurrent parent through marker-assisted selection, as well as near-isogenic lines (NILs) by selfing BC3F3 plants carrying different heterozygous segments for the QFLANG-4B region. We obtained eight recombinant types for QFLANG-4B, narrowing its location down to a 5.3-Mb region. This region contained 76 predicted genes, 7 of which we considered to be likely candidate genes for QFLANG-4B. Marker and phenotypic analyses of individual plants from the secondary mapping populations and their progeny revealed that the FLANG of the ND3331 allele is significantly higher than that of the Zang1817 allele in multiple environments. These results not only provide a basis for the map-based cloning of QFLANG-4B, but also indicate that QFLANG-4B has great potential for marker-assisted selection in wheat breeding programs designed to improve plant architecture and yield.

QTL Mapping for Agronomic Important Traits in Well-Adapted Wheat Cultivars

Wheat (Triticum aestivum L.) is one of the most important food crops worldwide and provides the staple food for 40% of the world’s population. Increasing wheat production has become an important goal to ensure global food security. The grain yield of wheat is a complex trait that is usually influenced by multiple agronomically important traits. Thus, the genetic dissection and discovery of quantitative trait loci (QTL) of wheat-yield-related traits are very important to develop high-yield cultivars to improve wheat production. To analyze the genetic basis and discover genes controlling important agronomic traits in wheat, a recombinant inbred lines (RILs) population consisting of 180 RILs derived from a cross between Xinong822 (XN822) and Yannong999 (YN999), two well-adapted cultivars, was used to map QTL for plant height (PH), spike number per spike (SNS), spike length (SL), grain number per spike (GNS), spike number per plant (SN), 1000- grain weight (TGW), grain length (GL), grain width (GW), length/width of grain (GL/GW), perimeter of grain (Peri), and surface area of grains (Sur) in three environments. A total of 64 QTL were detected and distributed on all wheat chromosomes except 3A and 5A. The identified QTL individually explained 2.24–38.24% of the phenotypic variation, with LOD scores ranging from 2.5 to 29. Nine of these QTL were detected in multiple environments, and seven QTL were associated with more than one trait. Additionally, Kompetitive Allele Specific PCR (KASP) assays for five major QTL QSns-1A.2 (PVE = 6.82), QPh-2D.1 (PVE = 37.81), QSl-2D (PVE = 38.24), QTgw-4B (PVE = 8.78), and QGns-4D (PVE = 13.54) were developed and validated in the population. The identified QTL and linked markers are highly valuable in improving wheat yield through marker-assisted breeding, and the large-effect QTL can be fine-mapped for further QTL cloning of yield-related traits in wheat.

Sub1 QTL confers submergence tolerance in rice through nitro-oxidative regulation and phytohormonal signaling

Constant change in global climate has become the most important limiting factor to crop productivity. Asymmetrical precipitations are causing recurrent flood events around the world. Submergence is one of the most detrimental abiotic stresses for sustainable rice production in the rainfed ecosystems of Southeast Asia. Therefore, the development of submergence-tolerant rice is an essential requirement to encounter food security. Submergence tolerance in rice is governed by the major quantitative trait locus (QTL) designated as Submergence1 (Sub1) near the centromere of chromosome 9. The introduction of the Sub1 in high-yielding rice varieties producing near-isogenic lines (NILs) has shown extreme submergence tolerance. The present study aimed to understand the responses of rice genotype IR64 and its Sub1 NIL IR64 Sub1 following one week of complete submergence treatment. Submergence imposed severe nitro-oxidative stress in both the rice genotypes, consequently disrupting the cellular redox homeostasis. In this study, IR64 exhibited higher NADPH oxidase activity accompanied by increased reactive oxygen species, reactive nitrogen species, and malondialdehyde buildups and cell death under submergence. Higher accumulations of 1-Aminocyclopropane-1-carboxylic acid, gibberellic acid, and Indole-3-acetic acid were also observed in IR64 which accelerated the plant growth and root cortical aerenchyma development following submergence. In contrast, IR64 Sub1 had enhanced submergence tolerance associated with an improved antioxidant defense system with sustainable morpho-physiological activities and restricted root aerenchyma formation. The comprehensive analyses of the responses of rice genotypes with contrasting submergence tolerance may demonstrate the intricacies of rice under complete submergence and may potentially contribute to improving stress resilience by advancing our understanding of the mechanisms of submergence tolerance in rice.

Identification of Quantitative Trait Loci Controlling Root Morphological Traits in an Interspecific Soybean Population Using 2D Imagery Data.

Roots are the hidden and most important part of plants. They serve as stabilizers and channels for uptaking water and nutrients and play a crucial role in the growth and development of plants. Here, two-dimensional image data were used to identify quantitative trait loci (QTL) controlling root traits in an interspecific mapping population derived from a cross between wild soybean 'PI366121' and cultivar 'Williams 82'. A total of 2830 single-nucleotide polymorphisms were used for genotyping, constructing genetic linkage maps, and analyzing QTLs. Forty-two QTLs were identified on twelve chromosomes, twelve of which were identified as major QTLs, with a phenotypic variation range of 36.12% to 39.11% and a logarithm of odds value range of 12.01 to 17.35. Two significant QTL regions for the average diameter, root volume, and link average diameter root traits were detected on chromosomes 3 and 13, and both wild and cultivated soybeans contributed positive alleles. Six candidate genes, Glyma.03G027500 (transketolase/glycoaldehyde transferase), Glyma.03G014500 (dehydrogenases), Glyma.13G341500 (leucine-rich repeat receptor-like protein kinase), Glyma.13G341400 (AGC kinase family protein), Glyma.13G331900 (60S ribosomal protein), and Glyma.13G333100 (aquaporin transporter) showed higher expression in root tissues based on publicly available transcriptome data. These results will help breeders improve soybean genetic components and enhance soybean root morphological traits using desirable alleles from wild soybeans.

QTL for the Kinematic Traits That Define the Arabidopsis Root Elongation Zone and Their Relationship to Gravitropism.

Cell expansion in a discrete region called the elongation zone drives root elongation. Analyzing time lapse images can quantify the expansion in kinematic terms as if it were fluid flow. We used horizontal microscopes to collect images from which custom software extracted the length of the elongation zone, the peak relative elemental growth rate (REGR) within it, the axial position of the REGR peak, and the root elongation rate. Automation enabled these kinematic traits to be measured in 1575 Arabidopsis seedlings representing 162 recombinant inbred lines (RILs) derived from a cross of Cvi and Ler ecotypes. We mapped ten quantitative trait loci (QTL), affecting the four kinematic traits. Three QTL affected two or more traits in these vertically oriented seedlings. We compared this genetic architecture with that previously determined for gravitropism using the same RIL population. The major QTL peaks for the kinematic traits did not overlap with the gravitropism QTL. Furthermore, no single kinematic trait correlated with quantitative descriptors of the gravitropism response curve across this population. In addition to mapping QTL for growth zone traits, this study showed that the size and shape of the elongation zone may vary widely without affecting the differential growth induced by gravity.

Genetic analysis and QTL mapping for pericarp thickness in maize (Zea mays L.)

Proper pericarp thickness protects the maize kernel against pests and diseases, moreover, thinner pericarp improves the eating quality in fresh corn. In this study, we aimed to investigate the dynamic changes in maize pericarp during kernel development and identified the major quantitative trait loci (QTLs) for maize pericarp thickness. It was observed that maize pericarp thickness first increased and then decreased. During the growth and formation stages, the pericarp thickness gradually increased and reached the maximum, after which it gradually decreased and reached the minimum during maturity. To identify the QTLs for pericarp thickness, a BC4F4 population was constructed using maize inbred lines B73 (recurrent parent with thick pericarp) and Baimaya (donor parent with thin pericarp). In addition, a high-density genetic map was constructed using maize 10 K SNP microarray. A total of 17 QTLs related to pericarp thickness were identified in combination with the phenotypic data. The results revealed that the heritability of the thickness of upper germinal side of pericarp (UG) was 0.63. The major QTL controlling UG was qPT1-1, which was located on chromosome 1 (212,215,145–212,948,882). The heritability of the thickness of upper abgerminal side of pericarp (UA) was 0.70. The major QTL controlling UA was qPT2-1, which was located on chromosome 2 (2,550,197–14,732,993). In addition, a combination of functional annotation, DNA sequencing analysis and quantitative real-time PCR (qPCR) screened two candidate genes, Zm00001d001964 and Zm00001d002283, that could potentially control maize pericarp thickness. This study provides valuable insights into the improvement of maize pericarp thickness during breeding.

Genetic dissection of rice resistance to bacterial blight

Bacterial blight, a major disease in rice, poses a serious impact on rice production. In this study, a doubled haploid (DH) population derived from a cross between the introduced japonica cultivar 'Maybelle' and the indica landrace 'Baiyeqiu' was used to investigate the pathogenicity of four pathogen races causing bacterial blight. The results showed that the pathogenicity of all the pathogen races exhibited continuous, transgressive distribution in the DH population. Moreover, strong correlations existed between every two pathogen races, with the correlation coefficients ranging from 0.3 to 0.6. A total of 12 quantitative trait loci (QTLs) distributed on chromosomes 1, 2, 3, 5, 6, 7, 9, and 12 were detected for rice bacterial blight, explaining 4.95% to 16.05% of the phenotype. Among these QTLs, a major QTL located in the interval RM6024-RM163 on chromosome 5 was detected in three pathogen races. In addition, the pyramiding of the positive alleles can apparently improve the rice resistance to bacterial blight. This study is of great significance for broadening the genetic resources with resistance to bacterial blight in China.

QTL mapping for the flag leaf-related traits using RILs derived from Trititrigia germplasm line SN304 and wheat cultivar Yannong15 in multiple environments

BackgroundDeveloping and enriching genetic resources plays important role in the crop improvement. The flag leaf affects plant architecture and contributes to the grain yield of wheat (Triticum aestivum L.). The genetic improvement of flag leaf traits faces problems such as a limited genetic basis. Among the various genetic resources of wheat, Thinopyrum intermedium has been utilized as a valuable resource in genetic improvement due to its disease resistance, large spikes, large leaves, and multiple flowers. In this study, a recombinant inbred line (RIL) population was derived from common wheat Yannong15 and wheat-Th. intermedium introgression line SN304 was used to identify the quantitative trait loci (QTL) for flag leaf-related traits.ResultsQTL mapping was performed for flag leaf length (FLL), flag leaf width (FLW) and flag leaf area (FLA). A total of 77 QTLs were detected, and among these, 51 QTLs with positive alleles were contributed by SN304. Fourteen major QTLs for flag leaf traits were detected on chromosomes 2B, 3B, 4B, and 2D. Additionally, 28 QTLs and 8 QTLs for flag leaf-related traits were detected in low-phosphorus and drought environments, respectively. Based on major QTLs of positive alleles from SN304, we identified a pair of double-ended anchor primers mapped on chromosome 2B and amplified a specific band of Th. intermedium in SN304. Moreover, there was a major colocated QTL on chromosome 2B, called QFll/Flw/Fla-2B, which was delimited to a physical interval of approximately 2.9 Mb and contained 20 candidate genes. Through gene sequence and expression analysis, four candidate genes associated with flag leaf formation and growth in the QTL interval were identified.ConclusionThese results promote the fine mapping of QFll/Flw/Fla-2B, which have pleiotropic effects, and will facilitate the identification of candidate genes for flag leaf-related traits. Additionally, this work provides a theoretical basis for the application of Th. intermedium in wheat breeding.

Characterization of a wheat stable QTL for spike length and its genetic effects on yield-related traits

Spike length (SL) is one of the most important agronomic traits affecting yield potential and stability in wheat. In this study, a major stable quantitative trait locus (QTL) for SL, i.e., qSl-2B, was detected in multiple environments in a recombinant inbred line (RIL) mapping population, KJ-RILs, derived from a cross between Kenong 9204 (KN9204) and Jing 411 (J411). The qSl-2B QTL was mapped to the 60.06–73.06 Mb region on chromosome 2B and could be identified in multiple mapping populations. An InDel molecular marker in the target region was developed based on a sequence analysis of the two parents. To further clarify the breeding use potential of qSl-2B, we analyzed its genetic effects and breeding selection effect using both the KJ-RIL population and a natural mapping population, which consisted of 316 breeding varieties/advanced lines. The results showed that the qSl-2B alleles from KN9204 showed inconsistent genetic effects on SL in the two mapping populations. Moreover, in the KJ-RILs population, the additive effects analysis of qSl-2B showed that additive effect was higher when both qSl-2D and qSl-5A harbor negative alleles under LN and HN. In China, a moderate selection utilization rate for qSl-2B was found in the Huanghuai winter wheat area and the selective utilization rate for qSl-2B continues to increase. The above findings provided a foundation for the genetic improvement of wheat SL in the future via molecular breeding strategies.

Genome-wide association analysis of eggshell color of an F2 generation population reveals candidate genes in chickens

Eggshell color is an important visual characteristic that affects consumer preferences for eggs. Eggshell color, which has moderate to high heritability, can be effectively enhanced through molecular marker selection. Various studies have been conducted on eggshell color at specific time points. However, few longitudinal data are available on eggshell color. Therefore, the objective of this study was to investigate eggshell color using the Commission International de L'Eclairage L*a*b* system with multiple measurements at different ages (age at the first egg and at 32, 36, 40, 44, 48, 52, 56, 60, 66, and 72 weeks) within the same individuals from an F2 resource population produced by crossing White Leghorn and Dongxiang Blue chicken. Using an Affymetrix 600 single nucleotide polymorphism (SNP) array, we estimated the genetic parameters of the eggshell color trait, performed genome-wide association studies (GWASs), and screened for the potential candidate genes. The results showed that pink-shelled eggs displayed a significant negative correlation between L* values and both a* and b* values. Genetic heritability based on SNPs showed that the heritability of L*, a*, and b* values ranged from 0.32 to 0.82 for pink-shelled eggs, indicating a moderate to high level of genetic control. The genetic correlations at each time point were mostly above 0.5. The major-effect regions affecting the pink eggshell color were identified in the 10.3–13.0 Mb interval on Gallus gallus chromosome 20, and candidate genes were selected, including SLC35C2, PCIF1, and SLC12A5. Minor effect polygenic regions were identified on chromosomes 1, 6, 9, 12, and 15, revealing 11 candidate genes, including MTMR3 and SLC35E4. Members of the solute carrier family play an important role in influencing eggshell color. Overall, our findings provide valuable insights into the phenotypic and genetic aspects underlying the variation in eggshell color. Using GWAS analysis, we identified multiple quantitative trait loci (QTLs) for pink eggshell color, including a major QTL on chromosome 20. Genetic variants associated with eggshell color may be used in genomic breeding programs.

Mapping and validation of Fusarium wilt race 2 resistance QTL from Citrullus amarus line USVL246-FR2

Key messageFon race 2 resistant QTLs were identified on chromosomes 8 and 9. Families homozygous for resistance alleles at a haplotype of three KASP markers had 42% lower disease severity than those with susceptible alleles in an independent, interspecific validation population confirming their utility for introgression of Fusarium wilt resistance.Fusarium oxysporum f. sp. niveum (Fon) race 2 causes Fusarium wilt in watermelon and threatens watermelon production worldwide. Chemical management options are not effective, and no resistant edible watermelon cultivars have been released. Implementation of marker-assisted selection to develop resistant cultivars requires identifying sources of resistance and the underlying quantitative trait loci (QTL), developing molecular markers associated with the QTL, and validating marker-phenotype associations with an independent population. An intraspecific Citrullus amarus recombinant inbred line population from a cross of resistant USVL246-FR2 and susceptible USVL114 was used for mapping Fon race 2 resistance QTL. KASP markers were developed (N = 51) for the major QTL on chromosome 9 and minor QTL on chromosomes 1, 6, and 8. An interspecific F2:3 population was developed from resistance donor USVL246-FR2 (C. amarus) and a susceptible cultivar ‘Sugar Baby’ (Citrullus lanatus) to validate the utility of the markers for introgression of resistance from the wild crop relative into cultivated watermelon. Only 16 KASP markers segregated in the interspecific C. amarus/lanatus validation population. Four markers showed significant differences in the separation of genotypes based on family-mean disease severity, but together explained only 16% of the phenotypic variance. Genotypes that inherited homozygous resistant parental alleles at three KASP markers had 42% lower family-mean disease severity than homozygous susceptible genotypes. Thus, haplotype analysis was more effective at predicting the mean disease severity of families than single markers. The haplotype identified in this study will be valuable for developing Fon race 2 resistant watermelon cultivars.

Quantitative trait loci detection for three tiller-related traits and the effects on wheat (Triticum aestivum L.) yields.

A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for tiller-related traits were reported, and the candidate genes underlying qMtn-KJ-5D, a novel major and stable QTL for maximum tiller number, were characterized. Tiller-related traits play an important role in determining the yield potential of wheat. Therefore, it is important to elucidate the genetic basis for tiller number when attempting to use genetic improvement as a tool for enhancing wheat yields. In this study, a quantitative trait locus (QTL) analysis of three tiller-related traits was performed on the recombinant inbred lines (RILs) of a mapping population, referred to as KJ-RILs, that was derived from a cross between the Kenong 9204 (KN9204) and Jing 411 (J411) lines. A total of 38 putative additive QTLs and 55 pairwise putative epistatic QTLs for spike number per plant (SNPP), maximum tiller number (MTN), and ear-bearing tiller rate (EBTR) were detected in eight different environments. Among these QTLs with additive effects, three major and stable QTLs were first documented herein. Almost all but two pairwise epistatic QTLs showed minor interaction effects accounting for no more than 3.0% of the phenotypic variance. The genetic effects of two colocated major and stable QTLs, i.e., qSnpp-KJ-5D.1 and qMtn-KJ-5D, for yield-related traits were characterized. The breeding selection effect of the beneficial allele for the two QTLs was characterized, and its genetic effects on yield-related traits were evaluated. The candidate genes underlying qMtn-KJ-5D were predicted based on multi-omics data, and TraesKN5D01HG00080 was identified as a likely candidate gene. Overall, our results will help elucidate the genetic architecture of tiller-related traits and can be used to develop novel wheat varieties with high yields.

Transcriptome sequencing and expression analysis in peanut reveal the potential mechanism response to Ralstonia solanacearum infection

BackgroundBacterial wilt caused by Ralstonia solanacearum severely affects peanut (Arachis hypogaea L.) yields. The breeding of resistant cultivars is an efficient means of controlling plant diseases. Therefore, identification of resistance genes effective against bacterial wilt is a matter of urgency. The lack of a reference genome for a resistant genotype severely hinders the process of identification of resistance genes in peanut. In addition, limited information is available on disease resistance-related pathways in peanut.ResultsFull-length transcriptome data were used to generate wilt-resistant and -susceptible transcript pools. In total, 253,869 transcripts were retained to form a reference transcriptome for RNA-sequencing data analysis. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis of differentially expressed genes revealed the plant-pathogen interaction pathway to be the main resistance-related pathway for peanut to prevent bacterial invasion and calcium plays an important role in this pathway. Glutathione metabolism was enriched in wilt-susceptible genotypes, which would promote glutathione synthesis in the early stages of pathogen invasion. Based on our previous quantitative trait locus (QTL) mapping results, the genes arahy.V6I7WA and arahy.MXY2PU, which encode nucleotide-binding site-leucine-rich repeat receptor proteins, were indicated to be associated with resistance to bacterial wilt.ConclusionsThis study identified several pathways associated with resistance to bacterial wilt and identified candidate genes for bacterial wilt resistance in a major QTL region. These findings lay a foundation for investigation of the mechanism of resistance to bacterial wilt in peanut.

Genetic variability and QTL mapping of morphological traits and inflorescence prolificacy in African bermudagrass

AbstractAfrican bermudagrass (Cynodon transvaalensis Burtt‐Davy) (2n = 2x = 18) has unique morphological characteristics such as finer leaf blades and shorter internodes that are important to improving turf qualities (i.e., texture and density) as compared to other Cynodon species. It has been extensively used to cross with common bermudagrass (Cynodon dactylon Pers. var. dactylon) in developing high‐quality interspecific [C. dactylon (L.) Pers. × C. transvaalensis Burtt‐Davy] F1 hybrid cultivars for turf use. However, the molecular basis of its morphological variation is unknown. Accordingly, the objectives of this study were to estimate the heritability and identify quantitative trait loci (QTL) associated with morphological and reproductive traits. A first‐generation self‐pollinated (S1) population of 109 individuals was evaluated for plant height (PH), leaf blade width (LBW) and leaf blade length, stem internode diameter and length, and inflorescence prolificacy (IP) in a replicated field trial over three seasons (2018–2020). The broad‐sense heritability estimates ranged from 0.31 (PH) to 0.80 (IP). Twenty‐four QTL were identified and nine of them were consistent ones. Fifteen candidate genes were found at a major and consistent QTL region associated with LBW. Frequent QTL colocations were found among morphological traits and between morphological traits and IP, partially explaining the significant correlation. The findings provide critical information and resources toward understanding the genetic basis associated with morphological and reproductive traits within C. transvaalensis and could contribute to marker‐assisted selection for breeding new turf‐type bermudagrass cultivars.

Molecular mapping and candidate gene identification of two major quantitative trait loci associated with silique length in oilseed rape (Brassica napus L.).

The online version contains supplementary material available at 10.1007/s11032-024-01464-x.

Identification and validation of major and stable quantitative trait locus for falling number in common wheat (Triticum aestivum L.).

A major and stable QTL, QFn.sau-1B.2, which can explain 13.6% of the PVE in FN and has a positive effect on resistance in SGR, was mapped and validated. The falling number (FN) is considered one of the most important quality traits of wheat grain and is the most important quality evaluation index for wheat trade worldwide. The quantitative trait loci (QTLs) for FN were mapped in three years of experiments. 23, 30, and 58 QTLs were identified using the ICIM-BIP, ICIM-MET, and ICIM-EPI methods, respectively. Among them, seven QTLs were considered stable. QFn.sau-1B.2, which was mapped to the 1BL chromosome, can explain 13.6% of the phenotypic variation on average and is considered a major and stable QTL for FN. This QTL was mapped in a 1cM interval and is flanked by the markers AX-110409346 and AX-108743901. Epistatic analysis indicated that QFN.sau-1B.2 has a strong influence on FN through both additive and epistatic effects. The Kompetitive Allele-Specific PCR marker KASP-AX-108743901, which is closely linked to QFn.sau-1B.2, was designed. The genetic effect of QFn.sau-1B.2 on FN was successfully confirmed in Chuannong18 × T1208 and CN17 × CN11 populations. Moreover, the results of the additive effects of favorable alleles for FN showed that the QTLs for FN had significant effects not only on FN but also on the resistance to spike germination. Within the interval of QFn.sau-1B.2, 147 high-confidence genes were found. According to the gene annotation and the transcriptome data, four genes might be associated with FN. QFn.sau-1B.2 may provide a new resource for the high-quality breeding of wheat in the future.