QTL Fine Mapping Research Articles

Characterization of non-coding variants associated with transcription factor binding through ATAC-seq-defined footprint QTLs in liver.

Non-coding variants discovered by genome-wide association studies (GWAS) are enriched in regulatory elements harboring transcription factor (TF) binding motifs, strongly suggesting a connection between disease association and the disruption of cis-regulatory sequences. Occupancy of a TF inside a region of open chromatin can be detected in ATAC-seq where bound TFs block the transposase Tn5, leaving a pattern of relatively depleted Tn5 insertions known as a "footprint". Here, we sought to identify variants associated with TF-binding, or "footprint quantitative trait loci" (fpQTLs) in ATAC-seq data generated from 170 human liver samples. We used computational tools to scan the ATAC-seq reads to quantify TF binding likelihood as "footprint scores" at variants derived from whole genome sequencing generated in the same samples. We tested for association between genotype and footprint score and observed 693 fpQTLs associated with footprint-inferred TF binding (FDR < 5%). Given that Tn5 insertion sites are measured with base-pair resolution, we show that fpQTLs can aid GWAS and QTL fine-mapping by precisely pinpointing TF activity within broad trait-associated loci where the underlying causal variant is unknown. Liver fpQTLs were strongly enriched across ChIP-seq peaks, liver expression QTLs (eQTLs), and liver-related GWAS loci, and their inferred effect on TF binding was concordant with their effect on underlying sequence motifs in 80% of cases. We conclude that fpQTLs can reveal causal GWAS variants, define the role of TF binding site disruption in disease and provide functional insights into non-coding variants, ultimately informing novel treatments for common diseases.

Genetic Analysis and Fine Mapping of QTL for the Erect Leaf in Mutant mths29 Induced through Fast Neutron in Wheat.

The erect leaf plays a crucial role in determining plant architecture, with its growth and development regulated by genetic factors. However, there has been a lack of comprehensive studies on the regulatory mechanisms governing wheat lamina joint development, thus failing to meet current breeding demands. In this study, a wheat erect leaf mutant, mths29, induced via fast neutron mutagenesis, was utilized for QTL fine mapping and investigation of lamina joint development. Genetic analysis of segregating populations derived from mths29 and Jimai22 revealed that the erect leaf trait was controlled by a dominant single gene. Using BSR sequencing and map-based cloning techniques, the QTL responsible for the erect leaf trait was mapped to a 1.03 Mb physical region on chromosome 5A. Transcriptome analysis highlighted differential expression of genes associated with cell division and proliferation, as well as several crucial transcription factors and kinases implicated in lamina joint development, particularly in the boundary cells of the preligule zone in mths29. These findings establish a solid foundation for understanding lamina joint development and hold promise for potential improvements in wheat plant architecture.

Fine mapping and candidate gene analysis of a major QTL for grain length on chromosome 5BS in bread wheat

Large grain is a favorable trait for appearance quality and large sink potential in wheat breeding. A stable QTL QGl.caas-5BS for grain length was previously identified in a recombinant inbred line population from the cross of Zhongmai 871 (ZM871) and its sister line Zhongmai 895 (ZM895). Here, a BC1F6 residual heterozygous line was selected from the cross of ZM871/ZM895//ZM871 population, and six heterozygous recombinant plants were identified in the BC1F7 population from self-pollination of the heterozygous line. QGl.caas-5BS was delimited into an interval of approximately 2.2 Mb flanked by markers Kasp_5B33 and Kasp_5B2 (25.3-27.5 Mb) through phenotyping and genotyping the secondary mapping populations derived from these heterozygous recombinant plants. Five genes were predicted as candidates of QGl.caas-5BS based on sequence polymorphism and differential expression analyses. Further mutation analysis showed that TraesCS5B02G026800 is likely the causal gene of QGl.caas-5BS. A gene-specific marker Kasp_5B_Gl for TraesCS5B02G026800 was developed, and a significant genetic effect of QGl.caas-5BS on grain length was identified in a validation population including 166 cultivars using the marker. These findings lay a good foundation for map-based cloning of QGl.caas-5BS and provide a breeding-applicable marker for the improvement of grain length in wheat.

Two adjacent NLR genes conferring quantitative resistance to clubroot disease in Arabidopsis are regulated by a stably inherited epiallelic variation

Clubroot caused by the protist Plasmodiophora brassicae is a major disease affecting cultivated Brassicaceae. Using a combination of quantitative trait locus (QTL) fine mapping, CRISPR-Cas9 validation, and extensive analyses of DNA sequence and methylation patterns, we revealed that the two adjacent neighboring NLR (nucleotide-binding and leucine-rich repeat) genes AT5G47260 and AT5G47280 cooperate in controlling broad-spectrum quantitative partial resistance to the root pathogen P. brassicae in Arabidopsis and that they are epigenetically regulated. The variation in DNA methylation is not associated with any nucleotide variation or any transposable element presence/absence variants and is stably inherited. Variations in DNA methylation at the Pb-At5.2 QTL are widespread across Arabidopsis accessions and correlate negatively with variations in expression of the two genes. Our study demonstrates that natural, stable, and transgenerationally inherited epigenetic variations can play an important role in shaping resistance to plant pathogens by modulating the expression of immune receptors.

QTL analysis and fine mapping of a major QTL and identification of candidate genes controlling curd setting height in cauliflower

QTL analysis and fine mapping of a major QTL and identification of candidate genes controlling curd setting height in cauliflower

Fine mapping and candidate gene analysis of a major QTL for oil content in the seed of Brassica napus.

By integrating QTL fine mapping and transcriptomics, a candidate gene responsible for oil content in rapeseed was identified. The gene is anticipated to primarily function in photosynthesis and photosystem metabolism pathways. Brassica napus is one of the most important oil crops in the world, and enhancing seed oil content is an important goal in its genetic improvement. However, the underlying genetic basis for the important trait remains poorly understood in this crop. We previously identified a major locus, OILA5 responsible for seed oil content on chromosome A5 through genome-wide association study. To better understand the genetics of the QTL, we performed fine mapping of OILA5 with a double haploid population and a BC3F2 segregation population consisting of 6227 individuals. We narrowed down the QTL to an approximate 43kb region with twelve annotated genes, flanked by markers ZDM389 and ZDM337. To unveil the potential candidate gene responsible for OILA5, we integrated fine mapping data with transcriptome profiling using high and low oil content near-isogenic lines. Among the candidate genes, BnaA05G0439400ZS was identified with high expression levels in both seed and silique tissues. This gene exhibited homology with AT3G09840 in Arabidopsis that was annotated as cell division cycle 48. We designed a site-specific marker based on resequencing data and confirmed its effectiveness in both natural and segregating populations. Our comprehensive results provide valuable genetic information not only enhancing our understanding of the genetic control of seed oil content but also novel germplasm for advancing high seed oil content breeding in B. napus and other oil crops.

Integrating de novo QTL-seq and linkage mapping to identify quantitative trait loci conditioning physiological resistance and avoidance to white mold disease in dry bean.

White mold (WM), caused by the ubiquitous fungus Sclerotinia sclerotiorum, is a devastating disease that limits production and quality of dry bean globally. In the present study, classic linkage mapping combined with QTL-seq were employed in two recombinant inbred line (RIL) populations, "Montrose"/I9365-25 (M25) and "Raven"/I9365-31 (R31), with the initial goal of fine-mapping QTL WM5.4 and WM7.5 that condition WM resistance. The RILs were phenotyped for WM reactions under greenhouse (straw test) and field environments. The general region of WM5.4 and WM7.5 were reconfirmed with both mapping strategies within each population. Combining the results from both mapping strategies, WM5.4 was delimited to a 22.60-36.25 Mb interval in the heterochromatic regions on Pv05, while WM7.5 was narrowed to a 0.83 Mb (3.99-4.82 Mb) region on the Pv07 chromosome. Furthermore, additional QTL WM2.2a (3.81-7.24 Mb), WM2.2b (11.18-17.37 Mb, heterochromatic region), and WM2.2c (23.33-25.94 Mb) were mapped to a narrowed genomic interval on Pv02 and WM4.2 in a 0.89 Mb physical interval at the distal end of Pv04 chromosome. Gene models encoding gibberellin 2-oxidase proteins regulating plant architecture are likely candidate genes associated with WM2.2a resistance. Nine gene models encoding a disease resistance protein (quinone reductase family protein and ATWRKY69) found within the WM5.4 QTL interval are putative candidate genes. Clusters of 13 and 5 copies of gene models encoding cysteine-rich receptor-like kinase and receptor-like protein kinase-related family proteins, respectively, are potential candidate genes associated with WM7.5 resistance and most likely trigger physiological resistance to WM. Acquired knowledge of the narrowed major QTL intervals, flanking markers, and candidate genes provides promising opportunities to develop functional molecular markers to implement marker-assisted selection for WM resistant dry bean cultivars.

Genetic analysis and fine mapping of a grain size QTL in the small-grain sterile rice line Zhuo201S

The development and application of the small-grain rice sterile line Zhuo201S (Z201S) has demonstrated its potential for mechanized hybrid rice seed production, leading to significant cost reductions. However, the molecular mechanism responsible for the small-grain size characteristic of Z201S remains unclear. In this study, we conducted a genetic analysis using near-isogenic lines constructed from Z210S, a small-grain rice sterile line, and R2115, a normal-grain variety. The results revealed that the small-grain trait in Z201S is governed by a single partially dominant gene which also enhances grain number. Through mapping, we localized the causal gene to the short arm of chromosome 2, within a 113 kb physical region delimited by the molecular markers S2-4-1 and LB63. Transgenic analysis and gene expression assays indicated LOC_Os02g14760 as the most likely candidate gene, suggesting that the small-grain size trait of Z201S is controlled by a novel locus that has not been previously identified.

QTL study reveals candidate genes underlying host resistance in a Red Queen model system.

Specific interactions of host and parasite genotypes can lead to balancing selection, maintaining genetic diversity within populations. In order to understand the drivers of such specific coevolution, it is necessary to identify the molecular underpinnings of these genotypic interactions. Here, we investigate the genetic basis of resistance in the crustacean host, Daphnia magna, to attachment and subsequent infection by the bacterial parasite, Pasteuria ramosa. We discover a single locus with Mendelian segregation (3:1 ratio) with resistance being dominant, which we call the F locus. We use QTL analysis and fine mapping to localize the F locus to a 28.8-kb region in the host genome, adjacent to a known resistance supergene. We compare the 28.8-kb region in the two QTL parents to identify differences between host genotypes that are resistant versus susceptible to attachment and infection by the parasite. We identify 13 genes in the region, from which we highlight eight biological candidates for the F locus, based on presence/absence polymorphisms and differential gene expression. The top candidates include a fucosyltransferase gene that is only present in one of the two QTL parents, as well as several Cladoceran-specific genes belonging to a large family that is represented in multiple locations of the host genome. Fucosyltransferases have been linked to resistance in previous studies of Daphnia-Pasteuria and other host-parasite systems, suggesting that P. ramosa spore attachment could be mediated by changes in glycan structures on D. magna cuticle proteins. The Cladoceran-specific candidate genes suggest a resistance strategy that relies on gene duplication. Our results add a new locus to a growing genetic model of resistance in the D. magna-P. ramosa system. The identified candidate genes will be used in future functional genetic studies, with the ultimate aim to test for cycles of allele frequencies in natural populations.

Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement.

Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%-26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.

Molecular mapping for fruit-related traits, and joint identification of candidate genes and selective sweeps for seed size in melon.

Melon is a popular fruit vegetable crop worldwide with diverse morphological variation. We report a high-density genetic map of melon and nine major QTLs with physical region ranging from 43.47kb to 1.89Mb. Importantly, two seed-related trait QTLs were repeatedly detected in two environments, and the mapping region was narrowed to 522kb according to a regional linkage analysis. A total of 40 annotated genes were screened for nonsynonymous variations, of which EVM0009818, involved in cytokinin-activated signaling, was differentially expressed in the young fruits of parents based on RNA-seq. Selective sweep analysis identified 152 sweep signals for seed size, including the two seed-related QTLs and nine homologs that have been verified to regulate seed size in Arabidopsis or rice. This work illustrates the power of a joint analysis combining resequencing-based genetic map for QTL mapping and a combination of KASP genotyping and RNA-seq analysis to facilitate QTL fine mapping.

QTL identification, fine mapping, and marker development for breeding peanut (Arachis hypogaea L.) resistant to bacterial wilt

Key messageA major QTL, qBWA12, was fine mapped to a 216.68 kb physical region, and A12.4097252 was identified as a useful KASP marker for breeding peanut varieties resistant to bacterial wilt.Bacterial wilt, caused by Ralstonia solanacearum, is a major disease detrimental to peanut production in China. Breeding disease-resistant peanut varieties is the most economical and effective way to prevent the disease and yield loss. Fine mapping the QTLs for bacterial wilt resistance is critical for the marker-assisted breeding of disease-resistant varieties. A recombinant inbred population comprising 521 lines was used to construct a high-density genetic linkage map and to identify QTLs for bacterial wilt resistance following restriction-site-associated DNA sequencing. The genetic map, which included 5120 SNP markers, covered a length of 3179 cM with an average marker distance of 0.6 cM. Four QTLs for bacterial wilt resistance were mapped on four chromosomes. One major QTL, qBWA12, with LOD score of 32.8–66.0 and PVE of 31.2–44.8%, was stably detected in all four development stages investigated over the 3 trial years. Additionally, qBWA12 spanned a 2.7 cM region, corresponding to approximately 0.4 Mb and was fine mapped to a 216.7 kb region by applying KASP markers that were polymorphic between the two parents based on whole-genome resequencing data. In a large collection of breeding and germplasm lines, it was proved that KASP marker A12.4097252 can be applied for the marker-assisted breeding to develop peanut varieties resistant to bacterial wilt. Of the 19 candidate genes in the region covered by qBWA12, nine NBS-LRR genes should be further investigated regarding their potential contribution to the resistance of peanut against bacterial wilt.

Construction of a high-density genetic linkage map and QTL mapping for growth traits in hybrid Epinephelus fuscoguttatus (♀) and Epinephelus tukula (♂) progeny

QTL mapping is an effective method for marker assisted selection (MAS) in animal breeding, and high-density linkage genetic maps are necessary for fine mapping of QTLs. In this study, high-density genetic maps of hybrid Epinephelus fuscoguttatus (♀) and Epinephelus tukula (♂) progeny (which demonstrated improved growth rates compared with the female parent) were constructed using RAD technology. Sex-average, female-specific, and male-specific linkage maps were composed of 24 linkage groups (LGs). The genetic map developed in this study had the highest number of SNPs among reported genetic maps for groupers. The sex-average linkage map contained 2759 bin makers (150,468 SNPs) and spanned 1627.28 cM, with an average marker interval of 0.59 cM. The female-specific (E. fuscoguttatus) linkage map contained 648 bin makers (38,269 SNPs) and spanned 1414.68 cM, with an average marker interval of 2.22 cM. The male-specific (E. tukula) linkage map contained 2126 bin makers (112,015 SNPs) and spanned 1839.88 cM, with an average marker interval of 0.86 cM. In total, 45 QTLs comprising 318 SNPs for growth-related traits were identified, including 10 QTLs for body weight, 6 QTLs for full length, 7 QTLs for body length, 14 QTLs for head length, 5 QTLs for body height, and 3 QTLs for body thickness. In addition, 56 candidate genes related to growth, metabolism, bone formation, muscle development, and neural regulation were identified, including eight genes associated with growth in other fish. Among these, gpr126, fam20a, fam20c, sox9b, foxm1, foxl1, myf6, zbtb38, and sl should be a focus of further research. These results provide a foundation for fine QTL mapping in grouper, and theoretical guidance for exploring the causes of heterosis, which is of great significance for MAS in the breeding of hybrids and male and female parents.

Promoter variation in a homeobox gene, CpDll, is associated with deeply lobed leaf in Cucurbita pepo L.

CpDll, encoding an HD-Zip I transcription factor, positively regulates formation of deeply lobed leaf shape in zucchini, Cucurbita pepo, which is associated with sequence variation in its promoter region. Leaf shape is an important horticultural trait in zucchini (Cucurbita pepo L.). Deeply lobed leaves have potential advantages for high-density planting and hybrid production. However, little is known about the molecular basis of deeply lobed leaf formation in this important vegetable crop. Here, we conducted QTL analysis and fine mapping of the deeply lobed leaf (CpDll) locus using recombinant inbred lines and large F2 populations developed from crosses between the deeply lobed leaf HM-S2, and entire leaf Jin-GL parental lines. We show that CpDll exhibited incomplete dominance for the deeply lobed leaf shape in HM-S2. Map-based cloning provided evidence that CpCll encodes a type I homeodomain (HD)- and Leu zipper (Zip) element-containing transcription factor. Sequence analysis between HM-S2 and Jin-GL revealed no sequence variations in the coding sequences, whereas a number of variations were identified in the promoter region between them. DUAL-LUC assays revealed significantly stronger promoter activity in HM-S2 than that in Jin-GL. There was also significantly higher expression of CpDll in the leaf base of deeply lobed leaves of HM-S2 compared with entire leaf Jin-GL. Comparative analysis of CpDll gene homologs in nine cucurbit crop species (family Cucurbitaceae) revealed conservation in both structure and function of this gene in regulation of deeply lobed leaf formation. Our work provides new insights into the molecular basis of leaf lobe formation in pumpkin/squash and other cucurbit crops. This work also facilitates marker-assisted selection for leaf shape in zucchini breeding.

Genome resequencing-based high-density genetic map and QTL detection for yield and fiber quality traits in diploid Asiatic cotton (Gossypium arboreum)

Cotton is the most important fiber crop in the world. Asiatic cotton (Gossypium arboreum, genome A2) is a diploid cotton species producing spinnable fibers and important germplasm for cotton breeding and a significant model for fiber biology. However, the genetic map of Asiatic cotton has been lagging behind tetraploid cottons, as well as other stable crops. This study aimed to construct a high-density SNP genetic map and to map QTLs for important yield and fiber quality traits. Using a recombinant inbred line (RIL) population and genome resequencing technology, we constructed a high-density genetic map that covered 1980.17cM with an average distance of 0.61cM between adjacent markers. QTL analysis revealed a total of 297 QTLs for 13 yield and fiber quality traits in three environments, explaining 5.0-37.4% of the phenotypic variance, among which 75 were stably detected in two or three environments. Besides, 47 QTL clusters, comprising 131 QTLs for representative traits, were identified. Our works laid solid foundation for fine mapping and cloning of QTL for yield and fiber quality traits in Asiatic cotton.

Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.

A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp (Cyprinus carpio).

Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9–15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.

Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

“Synthetic recombinant” populations have emerged as a useful tool for dissecting the genetics of complex traits. They can be used to derive inbred lines for fine QTL mapping, or the populations themselves can be sampled for experimental evolution. In the latter application, investigators generally value maximizing genetic variation in constructed populations. This is because in evolution experiments initiated from such populations, adaptation is primarily fueled by standing genetic variation. Despite this reality, little has been done to systematically evaluate how different methods of constructing synthetic populations shape initial patterns of variation. Here we seek to address this issue by comparing outcomes in synthetic recombinant Saccharomyces cerevisiae populations created using one of two strategies: pairwise crossing of isogenic strains or simple mixing of strains in equal proportion. We also explore the impact of the varying the number of parental strains. We find that more genetic variation is initially present and maintained when population construction includes a round of pairwise crossing. As perhaps expected, we also observe that increasing the number of parental strains typically increases genetic diversity. In summary, we suggest that when constructing populations for use in evolution experiments, simply mixing founder strains in equal proportion may limit the adaptive potential.

Identification of Gray Leaf Spot Disease Candidate Gene in Narrow-Leafed Lupin (Lupinus angustifolius L.).

Selection for resistance against gray leaf spot (GLS) is a major objective in the lupin breeding programs. A segregation ratio of 1:1 (resistant:susceptible) in F8 recombinant inbred lines (RIL8) derived from a cross between a breeding line 83A:476 (resistant to GLS) and a wild accession P27255 (susceptible to GLS) indicated that GLS was controlled by a single major gene. To develop molecular markers linked to GLS, in the beginning, only 11 resistant lines and six susceptible lines from the 83A:476 and P27255 population were genotyped with MFLP markers, and three MFLP markers were identified to be co-segregated with GLS. This method was very efficient, but the markers were located outside of the gene, and could not be used in other germplasms. Then QTL analysis and fine mapping were conducted to identify the gene. Finally, the gene was narrowed down to a 241-kb region containing two disease resistance genes. To further identify the candidate gene, DNA variants between accessions Tanjil (resistant to GLS) and Unicrop (susceptible to GLS) were analyzed. The results indicated that only one SNP was detected in the 241 kb region. This SNP was located in the TMV resistance protein N-like gene region and also identified between 83A:476 and P27255. Genotyping the Tanjil/Unicrop RIL8 population showed that this SNP co-segregated with GLS resistance. The phylogenetic tree analysis of this gene among 18 lupin accessions indicates that Australian resistant breeding line/varieties were clustered into one group and carry two resistant alleles, while susceptible accessions were clustered into different groups.

Identification and Fine-Mapping of Quantitative Trait Loci Controlling Plant Height in Central European Winter Triticale (×Triticosecale Wittmack).

The quantitatively inherited trait plant height is routinely evaluated in triticale breeding programs as it substantially influences lodging and disease susceptibility, is a main contributor to biomass yield, and is required to improve hybrid seed production by fine-tuning plant height in the female and male parental pools in hybrid breeding programs. In this study, we evaluated a panel of 846 diverse Central European triticale genotypes to dissect the genetic architecture underlying plant height by genome-wide association mapping. This revealed three medium- to large-effect QTL on chromosomes 5A, 4B, and 5R. Genetic and physical fine-mapping of the putative QTL revealed that the QTL on chromosome 5R most likely corresponds to Ddw1 and that the QTL on chromosome 5A is likely to be Rht12. Furthermore, we observed a temporal trend in registered cultivars with a decreasing plant height during the past decades, accompanied by an increasing use of the height-reducing alleles at the identified QTL. In summary, our results shed new light on the genetic control of plant height in triticale and open new avenues for future improvement by breeding.