Stable Quantitative Trait Loci Research Articles

Unraveling the genetic basis of superior traits in Gossypium barbadense: From phenotype to genotype

G. barbadense is renowned for its high-quality fiber and is highly regarded as a natural material in the textile industry. However, research on cotton has mainly focused on G. hirsutum, and progress in sea island cotton has been relatively slow. There was limited understanding of the genetic loci and transcriptional regulatory mechanisms of important traits, and the genetic basis for the development of superior traits remains unclear. In this study, a recombinant inbred line (RIL) population was constructed using two sea island cotton parents from different cotton regions. The phenotypic characteristics of the two parents and the RIL population, as well as the phenotypic correlations, heritability, and genetic models of the RIL population, were comprehensively analyzed. The RIL population was genotyped using whole-genome resequencing technology, and a high-density intraspecific linkage map was constructed, consisting of 5295 bin markers and a total genetic map distance of 2721.79 centimorgans (cM). Phenotypic data collected from five different environments were used to detect 169 quantitative trait loci (QTLs) using the composite interval mapping method. Among these QTLs, 30 were related to agronomic traits, 61 were related to yield traits, and 78 were related to fiber quality traits. Additionally, 17 QTL clusters were detected, and the additive effects of these clusters explained the correlation between different phenotypic traits. Candidate genes for stable QTLs related to agronomic and yield traits were identified through variant annotation and functional prediction. Two bin markers associated with lint percentage (LP) were validated as potential breeding markers. Furthermore, using RNA-seq data of cotton fiber from the RIL population parents, the dynamic changes in gene expression during different developmental stages of cotton fiber were revealed, and important differentially expressed genes in the secondary cell wall development and metabolism network of fibers were identified. Importantly, through the combined analysis of fiber trait QTLs and transcriptomes, eight candidate genes involved in regulating fiber quality traits were predicted, and the genetic basis of the excellent allele site qFL_D04_1 in the breeding history of Chinese sea island cotton was elucidated. In summary, this study provides new genetic resources and potential breeding markers for cotton variety improvement, valuable theoretical information for understanding the genetic basis of important traits in sea island cotton, and effectively promotes the development of cotton biotechnology breeding.

Whole genome resequencing identifies candidate genes and allelic variation in the MdNADP-ME promoter that regulate fruit malate and fructose contents in apple

Soluble sugar and organic acids are key determinants of fruit organoleptic quality and directly affect the commodity value and economic returns of fruit crops. We conducted whole genome sequencing (WGS) of the apple varieties ‘Gala’ and ‘Xiahongrou’, along with their F1 hybrid, to construct a high-density bin map. Our quantitative genetic analysis pinpointed 53 quantitative trait loci (QTL)s related to 11 sugar and acid traits. We identified a candidate gene, MdNADP-ME, responsible for malate degradation, on a stable QTL of linkage group (LG) 15. Sequence analysis revealed an A/C SNP in the promoter region (MEp-799) that influences the binding of the transcription factor MdMYB2, impacting MdNADP-ME expression. In our study of various apple genotypes, this SNP was linked to malate and fructose levels. We also developed a dCAPS marker associated with fruit fructose content. These results substantiate the role of MdNADP-ME in maintaining the equilibrium of sugar and acid content in apple fruits.

An aldehyde dehydrogenase gene, GhALDH7B4_A06, positively regulates fiber strength in upland cotton (Gossypium hirsutum L.).

High fiber strength (FS) premium cotton has significant market demand. Consequently, enhancing FS is a major objective in breeding quality cotton. However, there is a notable lack of known functionally applicable genes that can be targeted for breeding. To address this issue, our study used specific length-amplified fragment sequencing combined with bulk segregant analysis to study FS trait in an F2 population. Subsequently, we integrated these results with previous quantitative trait locus mapping results regarding fiber quality, which used simple sequence repeat markers in F2, F2:3, and recombinant inbred line populations. We identified a stable quantitative trait locus qFSA06 associated with FS located on chromosome A06 (90.74-90.83 Mb). Within this interval, we cloned a gene, GhALDH7B4_A06, which harbored a critical mutation site in coding sequences that is distinct in the two parents of the tested cotton line. In the paternal parent Ji228, the gene is normal and referred to as GhALDH7B4_A06O; however, there is a nonsense mutation in the maternal parent Ji567 that results in premature termination of protein translation, and this gene is designated as truncated GhALDH7B4_A06S. Validation using recombinant inbred lines and gene expression analysis revealed that this mutation site is correlated with cotton FS. Virus-induced gene silencing of GhALDH7B4 in cotton caused significant decreases in FS and fiber micronaire. Conversely, GhALDH7B4_A06O overexpression in Arabidopsis boosted cell wall component contents in the stem. The findings of our study provide a candidate gene for improving cotton fiber quality through molecular 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.

Genetic insights into superior grain number traits: a QTL analysis of wheat-Agropyron cristatum derivative pubing3228

BackgroundAgropyron cristatum (L.) is a valuable genetic resource for expanding the genetic diversity of common wheat. Pubing3228, a novel wheat-A. cristatum hybrid germplasm, exhibits several desirable agricultural traits, including high grain number per spike (GNS). Understanding the genetic architecture of GNS in Pubing3228 is crucial for enhancing wheat yield. This study aims to analyze the specific genetic regions and alleles associated with high GNS in Pubing3228.MethodsThe study employed a recombination inbred line (RIL) population derived from a cross between Pubing3228 and Jing4839 to investigate the genetic regions and alleles linked to high GNS. Quantitative Trait Loci (QTL) analysis and candidate gene investigation were utilized to explore these traits.ResultsA total of 40 QTLs associated with GNS were identified across 16 chromosomes, accounting for 4.25–17.17% of the total phenotypic variation. Five QTLs (QGns.wa-1D, QGns.wa-5 A, QGns.wa-7Da.1, QGns.wa-7Da.2 and QGns.wa-7Da.3) accounter for over 10% of the phenotypic variation in at least two environments. Furthermore, 94.67% of the GNS QTL with positive effects originated from Pubing3228. Candidate gene analysis of stable QTLs identified 11 candidate genes for GNS, including a senescence-associated protein gene (TraesCS7D01G148000) linked to the most significant SNP (AX-108,748,734) on chromosome 7D, potentially involved in reallocating nutrients from senescing tissues to developing seeds.ConclusionThis study provides new insights into the genetic mechanisms underlying high GNS in Pubing3228, offering valuable resources for marker-assisted selection in wheat breeding to enhance yield.

Yield-related quantitative trait loci identification and lint percentage hereditary dissection under salt stress in upland cotton.

Salinity is frequently mentioned as a major constraint in worldwide agricultural production. Lint percentage (LP) is a crucial yield-component in cotton lint production. While the genetic factors affect cotton yield in saline soils are still unclear. Here, we employed a recombinant inbred line population in upland cotton (Gossypium hirsutum L.) and investigated the effects of salt stress on five yield and yield component traits, including seed cotton yield per plant, lint yield per plant, boll number per plant, boll weight, and LP. Between three datasets of salt stress (E1), normal growth (E2), and the difference values dataset of salt stress and normal conditions (D-value), 87, 82, and 55 quantitative trait loci (QTL) were detectable, respectively. In total, five QTL (qLY-Chr6-2, qBNP-Chr4-1, qBNP-Chr12-1, qBNP-Chr15-5, qLP-Chr19-2) detected in both in E1 and D-value were salt related QTL, and three stable QTL (qLP-Chr5-3, qLP-Chr13-1, qBW-Chr5-5) were detected both in E1 and E2 across 3 years. Silencing of nine genes within a stable QTL (qLP-Chr5-3) highly expressed in fiber developmental stages increased LP and decreased fiber length (FL), indicating that multiple minor-effect genes clustered on Chromosome 5 regulate LP and FL. Additionally, the difference in LP caused by Gh_A05G3226 is mainly in transcription level rather than in the sequence difference. Moreover, silencing of salt related gene (GhDAAT) within qBNP-Chr4-1 decreased salt tolerance in cotton. Our findings shed light on the regulatory mechanisms underlining cotton salt tolerance and fiber initiation.

Quantitative trait locus mapping of hawthorn flavonoid content based on high-density linkage map

Hawthorn (Crataegus pinnatifida Bunge) belongs to the Rosaceae family and possess important value in food and medicinal product. Flavonoids in hawthorn leaves are major active ingredients and widely used for medicinal purposes. In our study, leaves from hybrid populations of 'DMQ' × 'QJX' and 'DMQ' × 'XBRZ' were used for flavonoid content quantitative trait locus (QTL) mapping in 2018 and 2019 based on our previously established high-density genetic map. In total, 10 and 27 QTL related to leaf flavonoid content in 'DMQ' × 'QJX' were discovered in 2018 and 2019, respectively; 10 QTL related to leaf flavonoid content in 'DMQ' × 'XBRZ' were discovered in 2019. Interestingly, three stable QTL were obtained in the 'DMQ' × 'QJX' population, which were related to the content of Vi rhamnoside and Hy in 2018 and 2019 and co-segregated with three single nucleotide polymorphism markers: m2172, m516, and f258.The results of this study provide important theoretical reference for molecular assisted breeding of flavonoid trait in hawthorn.

Identification of two novel QTL for Fusarium head blight resistance in German wheat cultivar Centrum.

Fusarium head blight (FHB) is a devastating disease that occurs in warm and humid environments. The German wheat Centrum has displayed moderate to high levels of FHB resistance in the field for many years. In this study, an F6:8 recombinant inbred line (RIL) population derived from cross Centrum × Xinong 979 was evaluated for FHB response following point inoculation in five environments. The population and parents were genotyped using the GenoBaits Wheat 16 K Panel. Stable quantitative trait loci (QTL) associated with FHB resistance in Centrum were mapped on chromosome arms 2DS and 5BS. The most effective QTL, located in 2DS, was identified as a new chromosome region represented by a 1.4 Mb interval containing 17 candidate genes. Another novel QTL was mapped in chromosome arm 5BS of a 5BS-7BS translocation chromosome. In addition, two environmentally-sensitive QTL were mapped on chromosome arms 2BL from Centrum and 5AS from Xinong 979. Polymorphisms of flanking allele-specifc quantitative PCR (AQP) markers AQP-6 for QFhb.nwafu-2DS and 16K-13073 for QFhb.nwafu-5BS were validated in a panel of 217 cultivars and breeding lines. These markers could be useful for marker-assisted selection of FHB resistance and also provide a starting point for fine mapping and marker-based cloning of the resistance genes.

Genome-Wide Association Study Uncovers Genomic Regions Associated with Coleoptile Length in a Worldwide Collection of Oat.

The length of coleoptile is crucial for determining the sowing depth of oats in low-precipitation regions, which is significant for oat breeding programs. In this study, a diverse panel of 243 oat accessions was used to explore coleoptile length in two independent experiments. The panel exhibited significant variation in coleoptile length, ranging from 4.66 to 8.76 cm. Accessions from Africa, America, and the Mediterranean region displayed longer coleoptile lengths than those from Asia and Europe. Genome-wide association studies (GWASs) using 26,196 SNPs identified 34 SNPs, representing 32 quantitative trait loci (QTLs) significantly associated with coleoptile length. Among these QTLs, six were consistently detected in both experiments, explaining 6.43% to 10.07% of the phenotypic variation. The favorable alleles at these stable loci additively increased coleoptile length, offering insights for pyramid breeding. Gene Ontology (GO) analysis of the 350 candidate genes underlying the six stable QTLs revealed significant enrichment in cell development-related processes. Several phytochrome-related genes, including auxin transporter-like protein 1 and cytochrome P450 proteins, were found within these QTLs. Further validation of these loci will enhance our understanding of coleoptile length regulation. This study provides new insights into the genetic architecture of coleoptile length in oats.

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.

Identification of Candidate Genes for English Grain Aphid Resistance from QTLs Using a RIL Population in Wheat

The English grain aphid (EGA) (Sitobion avenae F.) is one of the most destructive species of aphids in wheat- (Triticum aestivum L.) planting areas worldwide. Large quantities of insecticides are usually used to control aphid damage. The identification of new EGA-resistant genes is necessary for sustainable wheat production. The objective of this study was to identify candidate genes for EGA resistance from stable quantitative trait loci (QTLs). We previously constructed a genetic map of unigenes (UG-Map) with 31,445 polymorphic sub-unigenes via the RNA sequencing of ‘TN18 × LM6’ recombinant inbred lines (TL-RILs). The relative aphid index (RAI) for the TL-RILs was investigated for two growing seasons, with three measured times (MTs) in each season. Using the UG-Map, 43 candidate genes were identified from 22 stable QTLs, with an average of 1.95 candidate genes per QTL. Among the 34 candidate genes annotated in the reference genome Chinese Spring (CS) RefSeq v1.1, the homologous genes of seven candidate genes, TraesCS1A02G-319900, TraesCS1B02G397300, TraesCS2D02G460800, TraesCS4A02G015600LC, TraesCS5B02G329200, TraesCS-6A02G000600 and TraesCS6A02G418600LC have been previously reported to play roles in aphid resistance. This suggests that these genes are strongly associated with EGA resistance in wheat. The candidate genes in this study should facilitate the cloning of EGA-resistant genes and genetic improvement in wheat breeding programs.

Identifying quantitative trait locus and candidate genes for maize (Zea mays L.) plant architecture traits based on segregating populations constructed by high‐generation sister lines

AbstractLeaf length, width and angle are important traits in the architecture of maize plants. Delving into the genetic mechanisms of these traits is of utmost significance for promoting population yield. In this study, we employed the high‐generation sister lines PCU and PCM, which have significant differences in leaf morphological traits, as parental entities for the creation of F2 and F2:3 populations. Through quantitative trait locus (QTL) mapping of the traits in the three ear leaves by ICIM, 55 QTL were obtained, with six stable QTL selected across divergent populations. These QTL had physical spans ranging from 0.34 to 44.8 Mbp. Through gene annotation and qRT‐PCR, Zm00001d007382, Zm00001d035965, Zm00001d042777 and Zm00001d020641 were predicted as potential candidates for regulating maize plant architecture. The results of this study lay a foundation for analysing the genetic mechanisms of maize plant architecture traits and cloning‐related genes.

Unveiling synergistic QTLs associated with slow wilting in soybean (Glycine max [L.] Merr.)

Key messageA stable QTL qSW_Gm10 works with a novel locus, qSW_Gm01, in a synergistic manner for controlling slow-wilting traits at the early vegetative stage under drought stress in soybean.Drought is one of the major environmental factors which limits soybean yield. Slow wilting is a promising trait that can enhance drought resilience in soybean without additional production costs. Recently, a Korean soybean cultivar SS2-2 was reported to exhibit slow wilting at the early vegetative stages. To find genetic loci responsible for slow wilting, in this study, quantitative trait loci (QTL) analysis was conducted using a recombinant inbred line (RIL) population derived from crossing between Taekwangkong (fast-wilting) and SS2-2 (slow-wilting). Wilting score and leaf moisture content were evaluated at the early vegetative stages for three years. Using the ICIM-MET module, a novel QTL on Chr01, qSW_Gm01 was identified, together with a previously known QTL, qSW_Gm10. These two QTLs were found to work synergistically for slow wilting of the RILs under the water-restricted condition. Furthermore, the SNP markers from the SoySNP50K dataset, located within these QTLs, were associated with the wilting phenotype in 30 diverse soybean accessions. Two genes encoding protein kinase 1b and multidrug resistance-associated protein 4 were proposed as candidate genes for qSW_Gm01 and qSW_Gm10, respectively, based on a comprehensive examination of sequence variation and gene expression differences in the parental lines under drought conditions. These genes may play a role in slow wilting by optimally regulating stomatal aperture. Our findings provide promising genetic resources for improving drought resilience in soybean and give valuable insights into the genetic mechanisms governing slow wilting.

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.

Identifying QTL for grain protein content independent from grain yield-related traits in durum wheat

Grain protein content (GPC) is a crucial quality trait determining the nutritional, rheological, and end-use properties characteristics of wheat. Breeding programs for GPC were hindered by complex genetic control, the strong influence of environmental factors, and the negative correlation between GPC and grain yield. To identify stable quantitative trait loci (QTL) associated with increased GPC without decreasing grain yield, a recombinant inbred lines population of durum wheat was genotyped with a 25K SNP array and evaluated for GPC and yield-related traits in four field trials. Six QTL for GPC were identified on chromosomes 1B, 2B (two loci), 4B, 5A, and 6A, consistently expressed across environments, four of which had antagonistic effects on grain yield per spike (GYS). Two QTL (QGpc.mgb-5A and QGpc/TKW.mgb-2B.2) on 2B and 5A chromosomes were independent of GYS variations and could be used in marker-assisted selection (MAS) for GPC improvement. Identifying and utilizing beneficial QTL/genes for wheat improvement requires careful consideration of the inverse relationship between GPC and yield-related traits, and phenotypic data collected across multiple environments. MAS or genomic selection techniques can effectively target favorable alleles for GPC enhancement while minimizing the impact on grain yield.

Meta-QTL analysis and candidate genes for quality traits, mineral content, and abiotic-related traits in wild emmer.

Wild emmer (Triticum turgidum ssp. dicoccoides) genotypes were studied for their high-nutritional value and good tolerance to various types of stress; for this reason, several QTL (quantitative trait loci) studies have been conducted to find favorable alleles to be introgressed into modern wheat cultivars. Given the complexity of the QTL nature, their interaction with the environment, and other QTLs, a small number of genotypes have been used in wheat breeding programs. Meta-QTL (MQTL) analysis helps to simplify the existing QTL information, identifying stable genomic regions and possible candidate genes for further allele introgression. The study aimed to identify stable QTL regions across different environmental conditions and genetic backgrounds using the QTL information of the past 14 years for different traits in wild emmer based upon 17 independent studies. A total of 41 traits were classified as quality traits (16), mineral composition traits (11), abiotic-related traits (13), and disease-related traits (1). The analysis revealed 852 QTLs distributed across all 14 chromosomes of wild emmer, with an average of 61 QTLs per chromosome. Quality traits had the highest number of QTLs (35%), followed by mineral content (33%), abiotic-related traits (28%), and disease-related traits (4%). Grain protein content (GPC) and thousand kernel weight (TKW) were associated with most of the QTLs detected. A total of 43 MQTLs were identified, simplifying the information, and reducing the average confidence interval (CI) from 22.6 to 4.78 cM. These MQTLs were associated with multiple traits across different categories. Nine candidate genes were identified for several stable MQTLs, potentially contributing to traits such as quality, mineral content, and abiotic stress resistance. These genes play essential roles in various plant processes, such as carbohydrate metabolism, nitrogen assimilation, cell wall biogenesis, and cell wall extensibility. Overall, this study underscores the importance of considering MQTL analysis in wheat breeding programs, as it identifies stable genomic regions associated with multiple traits, offering potential solutions for improving wheat varieties under diverse environmental conditions.

Fhb9, a major QTL for Fusarium head blight resistance improvement in wheat

Fusarium head blight (FHB), mainly caused by Fusarium graminearum, is one of the most devastating diseases of wheat worldwide. Identification and validation of major quantitative trait loci (QTLs) for FHB resistance without negative effects on agronomic traits is critical to success in breeding FHB-resistant cultivars. In this study, a stable major QTL on chromosome arm 2DL was identified by evaluating a recombinant inbred line (RIL) population derived from Shi4185×Shijiazhuang 8 in both field and greenhouse experiments. QTL mapping and pedigree analyses indicated that the 2DL QTL is the same QTL as QFhb-2DL previously identified in Ji5265, therefore, designated Fhb9. Four kompetitive amplicon sequence polymorphism (KASP) markers were developed based on exome capture sequencing data to enhance marker density in the Fhb9 region, and it was delimited to an interval between single nucleotide polymorphism (SNP) markers KASP-12056 (533.8) and KASP-525 (525.9 Mb) explained 26.0-30.1% of the phenotypic variation. Analysis of the geographic distribution of the Fhb9 resistance allele suggested that it originated from Huang-Huai winter wheat region in China, and very low frequency of Fhb9 in modern Chinese cultivars reveals that it has not been widely deployed in breeding programs. Field and greenhouse evaluation of yield-related traits of near-isogenic lines (NILs) contrasting in Fhb9 alleles indicated that Fhb9 resistance allele did not show any adverse effects on those traits. Fhb9 showed an additive effect on enhancing FHB resistance with Fhb1. Therefore, Fhb9 is a valuable major QTL for improving FHB resistance in wheat and the near-diagnostic markers developed in this study will facilitate its deployment in wheat breeding programs.

Fine mapping of a major QTL, qKl-1BL controlling kernel length in common wheat.

A major stable QTL, qKl-1BL, for kernel length of wheat was narrowed down to a 2.04-Mb interval on chromosome 1BL; the candidate genes were predicated and the genetic effects on yield-related traits were characterized. As a key factor influencing kernel weight, wheat kernel shape is closely related to yield formation, and in turn affects both wheat processing quality and market value. Fine mapping of the major quantitative trait loci (QTL) for kernel shape could provide genetic resources and a theoretical basis for the genetic improvement of wheat yield-related traits. In this study, a major QTL for kernel length (KL) on 1BL, named qKl-1BL, was identified from the recombinant inbred lines (RIL) in multiple environments based on the genetic map and physical map, with 4.76-21.15% of the phenotypic variation explained. To fine map qKl-1BL, the map-based cloning strategy was used. By using developed InDel markers, the near-isogenic line (NIL) pairs and eight key recombinants were identified from a segregating population containing 3621 individualsderived from residual heterozygous lines (RHLs)self-crossing. In combination with phenotype identification, qKl-1BL was finely positioned into a 2.04-Mb interval, KN1B:698.15-700.19Mb, with eight differentially expressed genes enriched at the key period of kernel elongation. Based on transcriptome analysis and functional annotation information, two candidate genes for qKl-1BL controlling kernel elongation were identified. Additionally, genetic effect analysis showed that the superior allele of qKl-1BL from Jing411 could increase KL, thousand kernel weight (TKW), and yield per plant (YPP) significantly, as well as kernel bulk density and stability time. Taken together, this study identified a QTL interval for controlling kernel length with two possible candidate genes, whichprovides an important basis for qKl-1BL cloning, functional analysis, and application in molecular breeding programs.

Detection of two homologous major QTLs and development of diagnostic molecular markers for sucrose content in peanut.

We identified two stable and homologous major QTLs for sucrose content in peanut, and developed breeder-friendly molecular markers for marker-assisted selection breeding. Sucrose content is a crucial quality trait for edible peanuts, and increasing sucrose content is a key breeding objective. However, the genetic basis of sucrose content in peanut remains unclear, and major quantitative trait loci (QTLs) for sucrose content have yet to be identified. In this study, a high-density genetic map was constructed based on whole-genome re-sequencing data from a peanut RIL population. This map consisted of 2,042 bins and 24,142 SNP markers, making it one of the most comprehensive maps to date in terms of marker density. Two major QTLs (qSCA06.2 and qSCB06.2) were identified, explaining 31.41% and 24.13% of the phenotypic variance, respectively. Notably, these two QTLs were located in homologous genomic regions between the A and B subgenomes. The elite allele of qSCA06.2 was exclusive to Valencia-type, while the elite allele of qSCB06.2 existed in other peanut types. Importantly, the distribution of alleles from two homologous QTLs in the RIL population and diverse germplasm accessions consistently demonstrated that only the combination of elite allelic genotypes from both QTLs/genes resulted in a significantly dominant phenotype, accompanied by a substantial increase in sucrose content. The newly developed diagnostic markers for these QTLs were confirmed to be reliable and could facilitate future breeding efforts to enhance sucrose content using marker-assisted selection techniques. Overall, this study highlights the co-regulation of sucrose content by two major homologous QTLs/genes and provides valuable insights into the genetic basis of sucrose in peanuts.

Dissection of a novel major stable QTL on chromosome 7D for grain hardness and its breeding value estimation in bread wheat.

Grain hardness (Gh) is important for wheat processing and end-product quality. Puroindolines polymorphism explains over 60% of Gh variation and the novel genetic factors remain to be exploited. In this study, a total of 153 quantitative trait loci (QTLs), clustered into 12 genomic intervals (C1-C12), for 13 quality-related traits were identified using a recombinant inbred line population derived from the cross of Zhongkemai138 (ZKM138) and Chuanmai44 (CM44). Among them, C7 (harboring eight QTLs for different quality-related traits) and C8 (mainly harboring QGh.cib-5D.1 for Gh) were attributed to the famous genes, Rht-D1 and Pina, respectively, indicating that the correlation of involved traits was supported by the pleotropic or linked genes. Notably, a novel major stable QTL for Gh was detected in the C12, QGh.cib-7D, with ZKM138-derived allele increasing grain hardness, which was simultaneously mapped by the BSE-Seq method. The geographic pattern and transmissibility of this locus revealed that the increasing-Gh allele is highly frequently present in 85.79% of 373 worldwide wheat varieties and presented 99.31% transmissibility in 144 ZKM138-derivatives, indicating the non-negative effect on yield performance and that its indirect passive selection has happened during the actual breeding process. Thus, the contribution of this new Gh-related locus was highlighted in consideration of improving the efficiency and accuracy of the soft/hard material selection in the molecular marker-assisted process. Further, TraesCS7D02G099400, TraesCS7D02G098000, and TraesCS7D02G099500 were initially deduced to be the most potential candidate genes of QGh.cib-7D. Collectively, this study provided valuable information of elucidating the genetic architecture of Gh for wheat quality improvement.