Major Quantitative Trait Loci Research Articles

The elite eating quality alleles Wxb and ALKb are regulated by OsDOF18 and coordinately improve head rice yield.

Head rice yield (HRY) measures rice milling quality and determines final grain yield and commercial value. Here, we report that two major quantitative trait loci for milling quality in rice, qMq-1 and qMq-2, represent allelic variants of Waxylv/Waxyb (hereafter Wx) encoding Granule-Bound Starch Synthase I (GBSSI) and Alkali Spreading Value ALKc/ALKb encoding Soluble Starch Synthase IIa (SSIIa), respectively. Complementation and overexpression transgenic lines in indica and japonica backgrounds confirmed that Wx and ALK coordinately regulate HRY by affecting amylose content, the number of amylopectin branches, amyloplast size, and thus grain filling and hardness. The transcription factor OsDOF18 acts upstream of Wx and ALK by activating their transcription. Furthermore, rice accessions with Wxb and ALKb alleles showed improved HRY over those with Wxlv and ALKc. Our study not only reveals the novel molecular mechanism underlying the formation of HRY but also provides a strategy for breeding rice cultivars with improved HRY.

Scald resistance in hybrid rye (Secale cereale): genomic prediction and GWAS.

Rye (Secale cereale L.) is an important cereal crop used for food, beverages, and feed, especially in North-Eastern Europe. While rye is generally more tolerant to biotic and abiotic stresses than other cereals, it still can be infected by several diseases, including scald caused by Rhynchosporium secalis. The aims of this study were to investigate the genetic architecture of scald resistance, to identify genetic markers associated with scald resistance, which could be used in breeding of hybrid rye and to develop a model for genomic prediction for scald resistance. Four datasets with records of scald resistance on a population of 251 hybrid winter rye lines grown in 2 years and at 3 locations were used for this study. Four genomic models were used to obtain variance components and heritabilities of scald resistance. All genomic models included additive genetic effects of the parental components of the hybrids and three of the models included additive-by-additive epistasis and/or dominance effects. All models showed moderate to high broad sense heritabilities in the range of 0.31 (SE 0.05) to 0.76 (0.02). The model without non-additive genetic effects and the model with dominance effects had moderate narrow sense heritabilities ranging from 0.24 (0.06) to 0.55 (0.08). None of the models detected significant non-additive genomic variances, likely due to a limited data size. A genome wide association study was conducted to identify markers associated with scald resistance in hybrid winter rye. In three datasets, the study identified a total of twelve markers as being significantly associated with scald resistance. Only one marker was associated with a major quantitative trait locus (QTL) influencing scald resistance. This marker explained 11-12% of the phenotypic variance in two locations. Evidence of genotype-by-environment interactions was found for scald resistance between one location and the other two locations, which suggested that scald resistance was influenced by different QTLs in different environments. Based on the results of the genomic prediction models and GWAS, scald resistance seems to be a quantitative trait controlled by many minor QTL and one major QTL, and to be influenced by genotype-by-environment interactions.

Identification of two major QTLs for pod shell thickness in peanut (Arachis hypogaea L.) using BSA-seq analysis.

Pod shell thickness (PST) is an important agronomic trait of peanut because it affects the ability of shells to resist pest infestations and pathogen attacks, while also influencing the peanut shelling process. However, very few studies have explored the genetic basis of PST. An F2 segregating population derived from a cross between the thick-shelled cultivar Yueyou 18 (YY18) and the thin-shelled cultivar Weihua 8 (WH8) was used to identify the quantitative trait loci (QTLs) for PST. On the basis of a bulked segregant analysis sequencing (BSA-seq), four QTLs were preliminarily mapped to chromosomes 3, 8, 13, and 18. Using the genome resequencing data of YY18 and WH8, 22 kompetitive allele-specific PCR (KASP) markers were designed for the genotyping of the F2 population. Two major QTLs (qPSTA08 and qPSTA18) were identified and finely mapped, with qPSTA08 detected on chromosome 8 (0.69-Mb physical genomic region) and qPSTA18 detected on chromosome 18 (0.15-Mb physical genomic region). Moreover, qPSTA08 and qPSTA18 explained 31.1-32.3% and 16.7-16.8% of the phenotypic variation, respectively. Fifteen genes were detected in the two candidate regions, including three genes with nonsynonymous mutations in the exon region. Two molecular markers (Tif2_A08_31713024 and Tif2_A18_7198124) that were developed for the two major QTL regions effectively distinguished between thick-shelled and thin-shelled materials. Subsequently, the two markers were validated in four F2:3 lines selected. The QTLs identified and molecular markers developed in this study may lay the foundation for breeding cultivars with a shell thickness suitable for mechanized peanut shelling.

Identification of major QTLs for drought tolerance in soybean, together with a novel candidate gene, GmUAA6.

Drought tolerance is a complex trait in soybean that is controlled by polygenetic quantitative trait loci (QTLs). In this study, wilting score, days-to-wilting, leaf relative water content, and leaf relative conductivity were used to identify QTLs associated with drought tolerance in recombinant inbred lines derived from a cross between a drought-sensitive variety, Lin, and a drought-tolerant variety, Meng. A total of 33 drought-tolerance QTLs were detected. Of these 17 were major QTLs. In addition, 15 were novel drought-tolerance QTLs. The most predominant QTL was on chromosome 11. This was detected in at least three environments. The overlapped mapping interval of the four measured traits was 0.2 cM in genetic distance (about 220 kb in physical length). Glyma.11g143500 (designated as GmUAA6), which encodes a UDP-N-acetylglucosamine transporter, was identified as the most likely candidate gene. The allele of GmUAA6 from Lin (GmUAA6Lin) was associated with improved soybean drought tolerance. Overexpression of GmUAA6Lin in Arabidopsis and soybean hairy roots enhanced drought tolerance. Furthermore, a 3-bp insertion/deletion (InDel) in the coding sequence of GmUAA6 explained up to 49.9% of the phenotypic variation in drought tolerance-related traits, suggesting that this InDel might be used in future marker-assisted selection of drought-tolerant lines in soybean breeding programs.

QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat.

Drought and heat frequently co-occur during crop growth leading to devastating yield loss. The knowledge of the genetic loci governing component traits of yield under combined drought and heat stress is essential for enhancing the climate resilience. The present study employed a mapping population of 180 recombinant inbred lines (RILs) derived from a cross between GW322 and KAUZ to identify quantitative trait loci (QTLs) governing the component traits of yield under heat and combined stress conditions. Phenotypic evaluation was conducted across two consecutive crop seasons (2021-2022 and 2022-2023) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at the Indian Council of Agricultural Research Institute-Indian Agricultural Research Institute (ICAR-IARI), New Delhi. Various physiological and agronomic traits of importance were measured. Genotyping was carried out with 35K SNP Axiom breeder's genotyping array. The linkage map spanned a length of 6769.45cM, ranging from 2.28cM/marker in 1A to 14.21cM/marker in 5D. A total of 35 QTLs were identified across 14 chromosomes with 6B containing the highest (seven) number of QTLs. Out of 35 QTLs, 16 were major QTLs explaining the phenotypic variance greater than 10%. The study identified eight stable QTLs along with two hotspots on chromosomes 6B and 5B. Five QTLs associated with traits thousand-grain weight (TGW), normalized difference vegetation index (NDVI), and plant height (PH) were successfully validated. Candidate genes encoding antioxidant enzymes, transcription factors, and growth-related proteins were identified in the QTL regions. In silico expression analysis highlighted higher expression of transcripts TraesCS2D02G021000.1, TraesCS2D02G031000, TraesCS6A02G247900, and TraesCS6B02G421700 under stress conditions. These findings contribute to a deeper understanding of the genetic architecture underlying combined heat and drought tolerance in wheat, providing valuable insights for wheat improvement strategies under changing climatic conditions.

Genetic dissection of major QTL for grain number per spike on chromosomes 5A and 6A in bread wheat (Triticum aestivum L.).

Grain number per spike (GNS) is a crucial component of grain yield and plays a significant role in improving wheat yield. To identify quantitative trait loci (QTL) associated with GNS, a recombinant inbred line (RIL) population derived from the cross of Zhongkemai 13F10 and Chuanmai 42 was employed to conduct QTL mapping across eight environments. Based on the bulked segregant exome sequencing (BSE-Seq), genomic regions associated with GNS were detected on chromosomes 5A and 6A. According to the constructed genetic maps, two major QTL QGns.cib-5A (LOD = 4.35-8.16, PVE = 8.46-14.43%) and QGns.cib-6A (LOD = 3.82-30.80, PVE = 5.44-12.38%) were detected in five and four environments, respectively. QGns.cib-6A is a QTL cluster for other seven yield-related traits. QGns.cib-5A and QGns.cib-6A were further validated using linked Kompetitive Allele Specific PCR (KASP) markers in different genetic backgrounds. QGns.cib-5A exhibited pleiotropic effects on productive tiller number (PTN), spike length (SL), fertile spikelet number per spike (FSN), and ratio of grain length to grain width (GL/GW) but did not significantly affect thousand grain weight (TGW). Haplotype analysis revealed that QGns.cib-5A and QGns.cib-6A were the targets of artificial selection during wheat improvement. Candidate genes for QGns.cib-5A and QGns.cib-6A were predicted by analyzing gene annotation, spatiotemporal expression patterns, and orthologous and sequence differences. These findings will be valuable for fine mapping and map-based cloning of genes underlying QGns.cib-5A and QGns.cib-6A.

Allelic combinations of Hd1, Hd16, and Ghd7 exhibit pleiotropic effects on agronomic traits in rice.

Heading date is a critical agronomic trait that significantly affects grain yield and quality in rice. As early heading is typically associated with reduced yield due to shorter growth duration, it is essential to harness optimum heading date genes and their allelic combinations to promote heading while minimizing yield penalties. In this study, we identified quantitative trait loci (QTLs) for heading date and other major agronomic traits in a recombinant inbred line (RIL) population derived from a cross between Koshihikari and Baegilmi. Analyses on 3 major QTLs for heading date and their underlying genes (Hd1, Hd16, and Ghd7) revealed their pleiotropic effects on culm length, panicle length, and head rice percentage. Additionally, Ghd7 exhibited pleiotropic effects on panicle number and grain size. Among 8 different types of allelic combinations of the 3 heading date genes, RILs carrying a single nonfunctional hd16 or ghd7 under the functional background of the other 2 genes (Hd1hd16Ghd7 and Hd1Hd16ghd7) showed potential for maintaining yield and quality-related traits while accelerating heading. These results provide valuable insights for fine-tuning heading dates in rice breeding programs.

Genetic Mapping, Identification, and Characterization of a Candidate Susceptibility Gene for Powdery Mildew in Cannabis sativa.

Powdery mildew (PM) in Cannabis sativa is most frequently caused by the biotrophic fungus Golovinomyces ambrosiae. Based on previously characterized variation in susceptibility to PM, biparental populations were developed by crossing the most resistant cultivar evaluated, 'FL 58', with a susceptible cultivar, 'TJ's CBD'. F1 progeny were evaluated and displayed a range of susceptibility, and two were self-pollinated to generate two F2 populations. In 2021, the F2 populations (n = 706) were inoculated with PM and surveyed for disease severity. In both F2 populations, 25% of the progeny were resistant, while the remaining 75% showed a range of susceptibility. The F2 populations, as well as selected F1 progeny and the parents, were genotyped with a single-nucleotide polymorphism array, and a consensus genetic map was produced. A major effect quantitative trait locus on C. sativa chromosome 1 (Chr01) and other smaller-effect quantitative trait loci (QTL) on four other chromosomes were identified. The most associated marker on Chr01 was located near CsMLO1, a candidate susceptibility gene. Genomic DNA and cDNA sequencing of CsMLO1 revealed a 6.8-kb insertion in FL 58, relative to TJ's CBD, of which 846 bp are typically spliced into the mRNA transcript encoding a premature stop codon. Molecular marker assays were developed using CsMLO1 sequences to distinguish PM-resistant and PM-susceptible genotypes. These data support the hypothesis that a mutated MLO susceptibility gene confers resistance to PM in C. sativa and provides new genetic resources to develop resistant cultivars. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-wide association analysis identifies a consistent QTL for powdery mildew resistance on chromosome 3A in Nordic and Baltic spring wheat

Key messageQPm.NOBAL-3A is an important QTL providing robust adult plant powdery mildew resistance in Nordic and Baltic spring wheat, aiding sustainable crop protection and breeding.Powdery mildew, caused by the biotrophic fungal pathogen Blumeria graminis f. sp. tritici, poses a significant threat to bread wheat (Triticum aestivum L.), one of the world’s most crucial cereal crops. Enhancing cultivar resistance against this devastating disease requires a comprehensive understanding of the genetic basis of powdery mildew resistance. In this study, we performed a genome-wide association study (GWAS) using extensive field trial data from multiple environments across Estonia, Latvia, Lithuania, and Norway. The study involved a diverse panel of recent wheat cultivars and breeding lines sourced from the Baltic region and Norway. We identified a major quantitative trait locus (QTL) on chromosome 3A, designated as QPm.NOBAL-3A, which consistently conferred high resistance to powdery mildew across various environments and countries. Furthermore, the consistency of the QTL haplotype effect was validated using an independent Norwegian spring wheat panel. Subsequent greenhouse seedling inoculations with 15 representative powdery mildew isolates on a subset of the GWAS panel indicated that this QTL provides adult plant resistance and is likely of race non-specific nature. Moreover, we developed and validated KASP markers for QPm.NOBAL-3A tailored for use in breeding. These findings provide a critical foundation for marker-assisted selection in breeding programs aimed at pyramiding resistance QTL/genes to achieve durable and broad-spectrum resistance against powdery mildew.

Genetic variation in ZmKW1 contributes to kernel weight and size in dent corn and popcorn.

Kernel weight is a critical factor that essentially affects maize (Zea mays) yield. In natural inbred lines, popcorn kernels exhibit overtly smaller sizes compared to dent corn kernels, and kernel weight, which is controlled by multiple genetic loci, varies widely. Here, we characterized a major quantitative trait locus on chromosome 1, responsible for controlling kernel weight (qKW1) andsize. The qKW1 locus encodes a protein containing a seven in absentia domain with E3 ubiquitin ligase activity, expressed prominently from the top to the middle region of the endosperm. The presence and function of qKW1 were confirmed through ZmKW1 gene editing, where the mutations in ZmKW1 within dent corn significantly increased kernel weight, consistent with alterations in kernel size, while overexpression of ZmKW1 had the opposite effect. ZmKW1 acts as a negative regulator of kernel weight and size by reducing both the number and size of the endosperm cells and impacting endosperm filling. Notably, the popcorn allele qKW1N and the dent corn allele qKW1D encode identical proteins; however, the differences in promoter activity arise due to the insertion of an Indel-1346 sequence in the qKW1N promoter, resulting in higher expression levels compared to qKW1D, thus contributing to the variation in kernel weight and size between popcorn and dent corn kernels. Linkage disequilibrium analysis of the 2.8 kb promoter region of ZmKW1 in a dataset comprising 111 maize association panels identified two distinct haplotypes. Our results provide insight into themechanisms underlying kernel development and yield regulation in dent corn and popcorn, with a specific focus on the role of the ubiquitinationsystem.

The MADS-box transcription factor CsAGL9 plays essential roles in seed setting in Camellia sinensis

The number of seed setting (NSS) is an important biological trait that affects tea propagation and yield. In this study, the NSS of an F1 tea population (n = 324) generated via a cross between ‘Longjing 43’ and ‘Baihaozao’ was investigated at two locations in two consecutive years. Quantitative trait locus (QTL) mapping of the NSS was performed, and 10 major QTLs were identified. In total, 318 genes were found in these 10 QTLs intervals, and 11 key candidate genes were preliminarily identified. Among them, the MADS-box transcription factor AGAMOUS LIKE 9 (CsAGL9, CSS0037962) located in the most stable QTL (qNSS2) was identified as a key gene affecting the NSS. CsAGL9 overexpression in Arabidopsis promoted early flowering and significantly decreased the length and number of pods and number of seeds per pod. Transcriptome analysis demonstrated that the auxin pathway, a key hormone pathway regulating plant reproduction, was highly affected in the transgenic lines. The auxin pathway was likewise the most prominent in the gene co-expression network study of CsAGL9 in tea plants. In summary, we identified CsAGL9 is essential for seed setting using QTL mapping integrated with RNA-seq, which shed a new light on the mechanism NSS of seed setting in tea plants.

Genetic Architecture of Body Fat Composition in Mice

Body fat composition is a quantitative measure of obesity, a major health concern in humans. Laboratory mice are considered an excellent model for dissecting the genetic basis of obesity due to the genetic variation present in inbred strains for body size and fat composition, as well as their historical use as a model organism for human disease studies. To identify the loci controlling fat pad weights and body weight in mice, we performed a quantitative trait loci (QTL) analysis of 513 (SM/J x NZB/BINJ) F2 individuals fed a high-fat diet for 14 weeks. Our analysis separated fat composition genetic effects from those affecting overall body sizes in mouse. Composite interval mapping (CIM) results showed that body weight was conditioned by three major additive QTLs, explaining 3 to 30% of the phenotypic variation. One significant QTL on chromosome 19 conditioned all fat pads with the exception of the inguinal fat weight, which was controlled by a different QTL also on chromosome 19. Significant QTLs associated with fat compositions were detected on chromosomes 17 and 19 and differed from those of body weight. The fat pad QTLs also showed mainly additive gene effects and they explained 2 to 7% of variation in fat composition. Joint analysis of correlated traits detected five additional large effect QTLs on five different linkage groups. These findings have indicated that fat composition and body weight in mouse are conditioned by one to three major additive genes and can therefore be potentially manipulated in controlling obesity.

Identification of major QTLs for seed size by combining QTL-mapping and RNAseq in an electron beam induced mutant of groundnut (Arachis hypogaea L.)

Combining QTL-mapping using SNP markers generated with genotyping by sequencing and RNA-seq identified a major QTL and candidate genes for enhanced seed size and leaf size in groundnut, respectively. Towards this, we conducted quantitative trait locus (QTL) analysis for hundred kernel weight in F2 mapping population derived from electron beam induced large seed mutant, TG 89 and normal seed genotype, ICGV 15007. A major QTL for seed size was identified in Arahy.05 chromosome between flanking markers AhMITE470 and SNP05_103140987. This QTL interval harboured a groundnut ortholog of TIFY gene. Of the 29 TIFY family genes in groundnut, the gene arahy.5M7JWE is the identified within the QTL interval on chromosome A05 and was down regulated in the mutant, indicating its putative role for large seed phenotype in the mutant.

Inheritance and molecular mapping of the genomic regions governing seedviability in soybean (Glycine max. L. Merr.)

Loos of seed viability in soybean (Glycine max L. Merrill, 2n=40) during ambient storage from harvest to the next planting season is a significant barrier for the production of high-quality seeds. The present study includes the inheritance and molecular mapping of the loci linked to seed viability in soybean. For this, five high viable genotypes (>90% germination after one year of storage) viz. EC-1023, EC-105790, G2651, UPSL34, UPSL736 and three poorly viable genotype (<70% germination after one year of storage) viz. MACS-565, PK1243, VLS61 were hybridized in all possible combination. Obtained F1 were advanced separately. Cross EC1023 x VLS61 and their derived F2:3 seeds, were exposed to 72 hours of accelerated ageing (AA) at 41°C and 100% RH, followed by a germination. After AA test, germination % of EC1023 and VL5-61 were 40 and 14, respectively, whereas range of F2:3 seeds were 4.16 to 71.42 %. The seed viability is governed by polygenes or quantitative trait loci (QTL), as evidenced by the continuous distribution of germination % of F2:3 seeds. Parental polymorphism was studied with 506 SSR markers indicated it to 20.35% whereas distribution of the polymorphism was not uniform across the chromosomes; Chr. 15 had 46.15% polymorphism as against 15.78% on Chr. 3 and 4. Through inclusive composite interval mapping 8 QTL for seed viability on Chr. 6, 7, 8, 10, 13 and 17, respectively, were mapped. Two of the eight QTLs appear to be major QTLs, as their PVE percent is greater than 10% and other seems as minor ones. Previously reported markers linked to seed viability were also validated in the parental genotypes, with only Satt538 being able to differentiate the five good and three poor storing genotypes. The genetics of seed viability, as well as the QTLs and markers found in this study, will pave the way for molecular breeding to generate genotypes with improved seed viability.

A QTL allele from wild soybean enhances protein content without reducing the oil content

Abstract Soybean is one of the chief crops producing protein and oil for human consumption. Wild soybean, the ancestor of cultivated soybean, possesses high seed protein content; therefore, it is a valuable genetic resource that could enhance protein content in the cultivated varieties. To identify the genes responsible for increasing protein content in wild soybean, a population comprising 113 BC4F6 chromosome segment substitution lines (CSSL) was developed from a cross between soybean cultivar ‘Jackson’ and wild soybean accession JWS156-1. The CSSL population was cultivated in the field conditions for 3 years (2018, 2019 and 2020), and the seeds harvested from each line were analysed for protein and oil contents by InfraTec Nova instrument. Quantitative trait locus (QTL) analysis with 243 SSR markers identified 12 QTLs associated with seed protein, oil and protein + oil contents. Among these QTLs, qPro8 and qPro19, two major and stable QTLs for protein content, were detected on chromosomes 8 and 19, respectively. No QTL for oil content was detected in the vicinity of qPro19, indicating that qPro19 did not influence the seed oil content. The effect of qPro19 was validated using near-isogenic lines (NILs) of qPro19. By introducing the qPro19 allele from wild soybean into another soybean variety, ‘Tachiyutaka’, a BC4 line, T-678, that showed enhanced seed protein content, without reducing the seed oil content. This study implied that the qPro19 allele from wild soybean could be a potential genetic resource for breeding programmes aimed to improve soybean seed quality.

Construction of a high-density genetic map for yardlong bean and identification of ANT1 as a regulator of anthocyanin biosynthesis.

Because its long, tender pods supply essential proteins, vitamins, and fibers to humans, yardlong bean (Vigna unguiculata ssp. sesquipedalis) is a commonly consumed vegetable, especially in Southeast Asia. To provide insights into the genetic bases of key agricultural traits in yardlong bean, we here created a high-density bin-map with 2084 bin markers using 514 227 SNPs from a recombinant-inbred line (RIL) population. Quantitative trait loci (QTL) mapping was carried out to identify loci associated with anthocyanin content (ANT), vitamin E content (VE), total soluble protein content (TSP), pod length (PL), hundred-seed weight (HSW), seed length and width (SL and SW, respectively), and seed coat color (SCC). In total, 20 related QTLs were isolated, explaining 7.58-56.03% of the phenotypic variation. Of these, five major QTLs (qANT5, qTSP11, qVE7, qPL3, and qSCC9) were detected in 2020, 2021, and the combined environment, explaining 11.96-56.03% of the phenotypic variation. VuANT1 was identified as a causal gene for the QTL qANT5, which regulated anthocyanin content; VuANT1 was highly expressed in immature purple pods but barely detectable in white pods. VuANT1 overexpression in tobacco leaves and yardlong bean hairy roots resulted in purple coloration as a result of anthocyanin accumulation. These findings suggested that VuANT1 was a key regulator of anthocyanin accumulation in yardlong bean. Our results lay a firm foundation for target agricultural trait improvement and clarification of the genetic mechanisms underlying agricultural traits in yardlong bean.

Identification of QTLs for resistance to 10 pathotypes of Plasmodiophora brassicae in Brassica oleracea cultivar ECD11 through genotyping-by-sequencing

Key messageTwo major quantitative trait loci (QTLs) and five minor QTLs for 10 pathotypes were identified on chromosomes C01, C03, C04 and C08 through genotyping-by-sequencing from Brassica oleracea.Clubroot caused by Plasmodiophora brassicae is an important disease in brassica crops. Managing clubroot disease of canola on the Canadian prairie is challenging due to the continuous emergence of new pathotypes. Brassica oleracea is considered a major source of quantitative resistance to clubroot. Genotyping-by-sequencing (GBS) was performed in the parental lines; T010000DH3 (susceptible), ECD11 (resistant) and 124 BC1 plants. A total of 4769 high-quality polymorphic SNP loci were obtained and distributed on 9 chromosomes of B. oleracea. Evaluation of 124 BC1S1 lines for resistance to 10 pathotypes: 3A, 2B, 5C, 3D, 5G, 3H, 8J, 5K, 5L and 3O of P. brassicae, was carried out. Seven QTLs, 5 originating from ECD11 and 2 from T010000DH3, were detected. One major QTL designated as Rcr_C03-1 on C03 contributed 16.0–65.6% of phenotypic variation explained (PVE) for 8 pathotypes: 2B, 5C, 5G, 3H, 8J, 5K, 5L and 3O. Another major QTL designated as Rcr_C08-1 on C08 contributed 8.3 and 23.5% PVE for resistance to 8J and 5K, respectively. Five minor QTLs designated as Rcr_C01-1, Rcr_C03-2, Rcr_C03-3, Rcr_C04-1 and Rcr_C08-2 were detected on chromosomes C01, C03, C04 and C08 that contributed 8.3–23.5% PVE for 5 pathotypes each of 3A, 2B, 3D, 8J and 5K. There were 1, 10 and 4 genes encoding TIR-NBS-LRR/CC-NBS-LRR class disease resistance proteins in the Rcr_C01-1, Rcr_C03-1 and Rcr_C08-1 flanking regions. The syntenic regions of the two major QTLs Rcr_C03-1 and Rcr_C08-1 in the B. rapa genome ‘Chiifu’ were searched.

Unraveling the genetic basis of grain number-related traits in a wheat-Agropyron cristatum introgressed line through high-resolution linkage mapping

BackgroundGrain number per spike (GNS) is a pivotal determinant of grain yield in wheat. Pubing 3228 (PB3228), a wheat-Agropyron cristatum germplasm, exhibits a notably higher GNS.ResultsIn this study, we developed a recombinant inbred line (RIL) population derived from PB3228/Gao8901 (PG-RIL) and constructed a high-density genetic map comprising 101,136 loci, spanning 4357.3 cM using the Wheat 660 K SNP array. The genetic map demonstrated high collinearity with the wheat assembly IWGSC RefSeq v1.0. Traits related to grain number and spikelet number per spike were evaluated in seven environments for quantitative trait locus (QTL) analysis. Five environmentally stable QTLs were detected in at least three environments. Among these, two major QTLs, QGns-4A.2 and QGns-1A.1, associated with GNS, exhibited positive alleles contributed by PB3228. Further, the conditional QTL analysis revealed a predominant contribution of PB3228 to the GNS QTLs, with both grain number per spikelet (GNSL) and spikelet number per spike (SNS) contributing to the overall GNS trait. Four kompetitive allele-specific PCR (KASP) markers that linked to QGns-4A.2 and QGns-1A.1 were developed and found to be effective in verifying the QTL effect within a diversity panel. Compared to previous studies, QGns-4A.2 exhibited stability across different trials, while QGns-1A.1 represents a novel QTL. The results from unconditional and conditional QTL analyses are valuable for dissecting the genetic contribution of the component traits to GNS at the individual QTL level and for understanding the genetic basis of the superior grain number character in PB3228. The KASP markers can be utilized in marker-assisted selection for enhancing GNS.ConclusionsFive environmentally stable QTLs related to grain number and spikelet number per spike were identified. PB3228 contributed to the majority of the QTLs associated with GNS.

Identification of QTL associated with resistance to Phytophthora fruit rot in cucumber (Cucumis sativus L.).

Phytophthora fruit rot (PFR) caused by the soilborne oomycete pathogen, Phytophthora capsici, can cause severe yield loss in cucumber. With no resistant variety available, genetic resources are needed to develop resistant varieties. The goal of this work was to identify quantitative trait loci (QTL) associated with resistance to PFR using multiple genomic approaches and populations. Two types of resistances have been identified: age-related resistance (ARR) and young fruit resistance. ARR occurs at 12-16 days post pollination (dpp), coinciding with the end of exponential fruit growth. A major QTL for ARR was discovered on chromosome 3 and a candidate gene identified based on comparative transcriptomic analysis. Young fruit resistance, which is observed during the state of rapid fruit growth prior to commercial harvest, is a quantitative trait for which multiple QTL were identified. The largest effect QTL, qPFR5.1, located on chromosome 5 was fine mapped to a 1-Mb region. Genome-wide association studies (GWAS) and extreme-phenotype genome-wide association study (XP-GWAS) for young fruit resistance were also performed on a cucumber core collection representing > 96% of the genetic diversity of the USDA cucumber germplasm. Several SNPs overlapped with the QTL identified from QTL-seq analysis on biparental populations. In addition, novel SNPs associated with the resistance were identified from the germplasm. The resistant alleles were found mostly in accessions from India and South Asia, the center of diversity for cucumber. The results from this work can be applied to future disease resistance studies and marker-assisted selection in breeding programs.

Fine mapping of qBK1.2, a major QTL governing resistance to bakanae disease in rice.

Bakanae disease caused by Fusarium fujikuroi is an emerging disease of rice causing losses in all rice-growing regions around the world. A BC2F2 population was developed by backcrossing the recurrent parent Pusa Basmati 1121 (PB1121) with the recombinant inbred line RIL28, which harbors a major quantitative trait locus (QTL) governing resistance to bakanae, qBK1.2. MassARRAY-based single-nucleotide polymorphism (SNP) assays targeting the genomic region of qBK1.2 helped in fine mapping the QTL to a region of 130 kb between the SNP markers rs3164311 and rs3295562 using 24 recombinants. In-silico mining of the fine-mapped region identified 11 putative candidate genes with functions related to defense. The expression analysis identified two significantly differentially expressed genes, that is, LOC_Os01g06750 and LOC_Os01g06870, between the susceptible genotype PB1121 and the resistant genotypes Pusa1342 and R-NIL4. Furthermore, the SNPs identified in LOC_Os01g06750 produced minor substitutions of amino acids with no major effect on the resistance-related functional motifs. However, LOC_Os01g06870 had 21 amino acid substitutions, which led to the creation of the leucine-rich repeat (LRR) domain in the resistant genotype Pusa1342, thereby making it a potential candidate underlying the major bakanae-resistant QTL qBK1.2. The markers used in the fine mapping program are of immense utility in marker-assisted breeding for bakanae resistance in rice.