Stable QTL Research Articles

Genetic dissection and validation of a stable QTL for grain roundness on chromosome 5A in bread wheat (Triticum aestivum L.)

Genetic dissection and validation of a stable QTL for grain roundness on chromosome 5A in bread wheat (Triticum aestivum L.)

GW3, encoding a member of the P450 subfamily, controls grain width by regulating the GA4 content in spikelets of rice (Oryza sativa L.).

A stable QTL, GW3, controlling grain width was identified in two populations. Its causal gene LOC_Os03g04680 was verified by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. Grain width (GW) is one of the key traits affecting grain size and determines grain yield and appearance quality in rice. Mining gene loci and elite alleles controlling GW is necessary. The GW phenotypes of the two populations were investigated in three environments, which showed abundant phenotypic variation. GW3, encoding a P450 subfamily protein, was identified and validated as a causal gene by gene-based haplotype analysis, expression analysis, gene knockout and complementation transgenic tests. The accessions with large GW values had high gene expression levels. In addition, the GW of the accessions with the GG allele was significantly greater than that of the accessions with the AA allele. The Hap 1 and Hap 3 were identified as elite haplotypes, which can increase GW. The expression levels of OsKO1, OsGA3ox1, OsGA20ox1 and OsGA20ox2 in the young panicle of A7444 were significantly greater than those in the young panicle of the mutants, indicating that GW3 may be involved in the gibberellins (GA) biosynthesis pathway to regulate GW. GA4 content detection and electron scanning analysis revealed that GA4 regulates GW by affecting glume cell size. These results provide new insights for studying the genetic mechanism of rice GW and provide a material basis for breeding high-yield rice varieties.

Integration Linkage Mapping and Comparative Transcriptome Analysis to Dissect the Genetic Basis of Rice Salt Tolerance Associated with the Germination Stage.

Soil salinity poses a serious threat to rice production. The salt tolerance of rice at the germination stage is one of the major determinants of stable stand establishment, which is very important for direct seeding in saline soil. The complexity and polygenic nature of salt tolerance have limited the efficiency of discovering and cloning key genes in rice. In this study, an RIL population with an ultra-high-density genetic map was employed to investigate the salt-tolerant genetic basis in rice, and a total of 20 QTLs were detected, including a major and stable QTL (qRCL3-1). Subsequently, salt-specific DEGs from a comparative transcriptome analysis were overlaid onto annotated genes located on a stable QTL interval, and eight putative candidate genes were further identified. Finally, from the sequence alignment and variant analysis, OsCam1-1 was confirmed to be the most promising candidate gene for regulating salinity tolerance in rice. This study provides important information for elucidating the genetic and molecular basis of rice salt tolerance at the germination stage, and the genes detected here will be useful for improvements in rice salt tolerance.

QTL Mapping of Yield, Agronomic, and Nitrogen-Related Traits in Barley (Hordeum vulgare L.) under Low Nitrogen and Normal Nitrogen Treatments.

Improving low nitrogen (LN) tolerance in barley (Hordeum vulgare L.) increases global barley yield and quality. In this study, a recombinant inbred line (RIL) population crossed between "Baudin × CN4079" was used to conduct field experiments on twenty traits of barley yield, agronomy, and nitrogen(N)-related traits under LN and normal nitrogen (NN) treatments for two years. This study identified seventeen QTL, comprising eight QTL expressed under both LN and NN treatments, eight LN-specific QTL, and one NN-specific QTL. The localized C2 cluster contained QTL controlling yield, agronomic, and N-related traits. Of the four novel QTL, the expression of the N-related QTL Qstna.sau-5H and Qnhi.sau-5H was unaffected by N treatment. Qtgw.sau-2H for thousand-grain weight, Qph.sau-3H for plant height, Qsl.sau-7H for spike length, and Qal.sau-7H for awn length were identified to be the four stable expression QTL. Correlation studies revealed a significant negative correlation between grain N content and harvest index (p < 0.01). These results are essential for barley marker-assisted selection (MAS) breeding.

Genome-wide association study and linkage mapping reveal TaqW-6B associated with water-extractable arabinoxylan content in wheat grain.

A novel QTL, TaqW-6B of water-extractable arabinoxylan content in the wheat grain on chromosome 6BL was identified and fine mapped in a narrow region 3.8Mb. Water-extractable arabinoxylan (WE-AX), an important component of hemicellulose, is associated with various abundant health benefits. In this study, QTLs for WE-AX content were detected in two populations: (1) a recombinant inbred line (RIL) population with 164 lines derived from a cross between Avocet and Chilero (AC population) genotyped with diversity array technology (DArT), and (2) a natural population of 243 varieties (CH population) genotyped with the Axiom wheat 660K single-nucleotide polymorphism (SNP) array. A stable QTL Qwe-ax.haust-6B, explaining 8.51-15.59% of the phenotypic variance, was mapped in the physical interval 459.38-572.09Mb on the long arm of chromosome 6B in the AC population, tightly linked with DArT markers 3,944,740 and 4,991,038 under three experimental conditions. The Qwe-ax.haust-6B was further narrowed down to be delimited in the physical interval 516.47-571.58Mb on chromosome 6BL, explaining 5.86-16.27% of the phenotypic variance in the CH population. Furthermore, we developed high-throughput kompetitive allele-specific PCR (KASP) markers to reconstruct the genetic linkage map in the AC population, and Qwe-ax.haust-6B was fine mapped into a narrow region named TaqW-6B, which was compressed between KASP-6B-3 and KASP-6B-6 at a physical distance of 3.8Mb. In the meanwhile, the markers were also validated in a natural population of 160 wheat lines (NP population). Consequently, this study is of great importance to provide the theoretical basis for cloning the key gene and developing functional markers for molecular breeding.

Envirotyping within a multi-environment trial allowed identifying genetic determinants of winter oilseed rape yield stability

Key messageA comprehensive environmental characterization allowed identifying stable and interactive QTL for seed yield: QA09 and QC09a were detected across environments; whereas QA07a was specifically detected on the most stressed environments.A main challenge for rapeseed consists in maintaining seed yield while adapting to climate changes and contributing to environmental-friendly cropping systems. Breeding for cultivar adaptation is one of the keys to meet this challenge. Therefore, we propose to identify the genetic determinant of seed yield stability for winter oilseed rape using GWAS coupled with a multi-environmental trial and to interpret them in the light of environmental characteristics. Due to a comprehensive characterization of a multi-environmental trial using 79 indicators, four contrasting envirotypes were defined and used to identify interactive and stable seed yield QTL. A total of four QTLs were detected, among which, QA09 and QC09a, were stable (detected at the multi-environmental trial scale or for different envirotypes and environments); and one, QA07a, was specifically detected into the most stressed envirotype. The analysis of the molecular diversity at QA07a showed a lack of genetic diversity within modern lines compared to older cultivars bred before the selection for low glucosinolate content. The results were discussed in comparison with other studies and methods as well as in the context of breeding programs.

Identification of new cotton fiber-quality QTL by multiple genomic analyses and development of markers for genomic breeding

Cotton fiber is one of the main raw materials for the textile industry. In recent years, many cotton fiber quality QTL have been identified, but few were applied in breeding. In this study, a genome wide association study (GWAS) of fiber-quality traits in 265 upland cotton breeding intermediate lines (GhBreeding), combined with genome-wide selective sweep analysis (GSSA) and genomic selection (GS), revealed 25 QTL. Most of these QTL were ignored by only using GWAS. The CRISPR/Cas9 mutants of GhMYB_D13 had shorter fiber, which indicates the credibility of QTL to a certain extent. Then these QTL were verified in other cotton natural populations, 5 stable QTL were found having broad potential for application in breeding. Additionally, among these 5 stable QTL, superior genotypes of 4 showed an enrichment in most improved new varieties widely cultivated currently. These findings provide insights for how to identify more QTL through combined multiple genomic analysis to apply in breeding.

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.

Quantitative trait loci identification reveals zinc finger protein CONSTANS-LIKE 4 as the key candidate gene of stigma color in watermelon (Citrullus lanatus)

Stigma color is a critical agronomic trait in watermelon that plays an important role in pollination. However, there are few reports on the regulation of stigma color in watermelon. In this study, a genetic analysis of the F2 population derived from ZXG1553 (P1, with orange stigma) and W1-17 (P2, with yellow stigma) indicated that stigma color is a quantitative trait and the orange stigma is recessive compared with the yellow stigma. Bulk segregant analysis sequencing (BSA-seq) revealed a 3.75 Mb segment on chromosome 6 that is related to stigma color. Also, a major stable effective QTL Clqsc6.1 (QTL stigma color) was detected in two years between cleaved amplified polymorphic sequencing (CAPS) markers Chr06_8338913 and Chr06_9344593 spanning a ~1.01 Mb interval that harbors 51 annotated genes. Cla97C06G117020 (annotated as zinc finger protein CONSTANS-LIKE 4) was identified as the best candidate gene for the stigma color trait through RNA-seq, quantitative real-time PCR (qRT-PCR), and gene structure alignment analysis among the natural watermelon panel. The expression level of Cla97C06G117020 in the orange stigma accession was lower than in the yellow stigma accessions with a significant difference. A nonsynonymous SNP site of the Cla97C06G117020 coding region that causes amino acid variation was related to the stigma color variation among nine watermelon accessions according to their re-sequencing data. Stigma color formation is often related to carotenoids, and we also found that the expression trend of ClCHYB (annotated as β-carotene hydroxylase) in the carotenoid metabolic pathway was consistent with Cla97C06G117020, and it was expressed in low amounts in the orange stigma accession. These data indicated that Cla97C06G117020 and ClCHYB may interact to form the stigma color. This study provides a theoretical basis for gene fine mapping and mechanisms for the regulation of stigma color in watermelon.

Identification of novel QTLs for resistance to late leaf spot in peanut by SNP array and QTL-seq

Late leaf spot (LLS) is one of important diseases that causes severe yield losses in peanut. Peanut has various sources of resistance to LLS, and the identification of resistant QTLs and the development of related molecular markers are of great importance for breeding of LLS-resistant peanut. In this study, 173 individual lines of a recombinant inbred line (RIL) population and 48K SNP array for genotyping were used to construct a high-density genetic map with 1475 SNP marker and 20 linkage groups. A total of 11 QTLs were obtained through QTL analysis using the constructed genetic map. Among them, a stable major QTL qLLS.LG02 was identified on linkage group 2 in all six environments, with a phenotypic variation explained (PVE) ranging from 15.57 to 31.09%. Additionally, QTL-seq technology was also employed for QTL analysis of LLS resistance. As a result, 14 QTL loci related to LLS resistance were identified using the G prime algorithm. Notably, physical position of qLLS02 and qLLS03 are coincided with that of qLLS.LG02 and qLLS.LG03 respectively. Gene annotation analysis within the 14 QTL intervals by QTL-seq revealed that there were a total of 163 NBS-LRR disease resistance genes, accounting for 22.86% of all R genes in peanut genome and showing a 4.26-fold enrichment with a p-value of 5.19e-57. Within the QTL region qLLS02 of the resistant parent Mi-2, there was a 5 Mb structural variation interval (SV) containing 81 NBS-LRR genes. A PCR diagnostic marker was developed, and validation data suggest that this SV might lead to gene deletion or replacement with other genes. This SV has the potential to enhance peanut resistance to late leaf spot disease. This study holds significant implications for improving peanut breeding for LLS resistance through development of associated molecular markers.

Aspartyl proteases identified as candidate genes of a fiber length QTL, qFLD05, that regulates fiber length in cotton (Gossypium hirsutum L.).

GhAP genes were identified as the candidates involved in cotton fiber length under the scope of fine mapping a stable fiber length QTL, qFLD05. Moreover, the transcription factor GhWRKY40 positively regulated GhAP3 to decrease fiber length. Fiber length (FL) is an economically important fiber quality trait. Although several genes controlling cotton fiber development have been identified, our understanding of this process remains limited. In this study, an FL QTL (qFLD05) was fine-mapped to a 216.9-kb interval using a secondary F2:3 population derived from the upland hybrid cultivar Ji1518. This mapped genomic segment included 15 coding genes, four of which were annotated as aspartyl proteases (GhAP1-GhAP4). GhAPs were identified as candidates for qFLD05 as the sequence variations in GhAPs were associated with FL deviations in the mapping population, and functional validation of GhAP3 and GhAP4 indicated a longer FL following decreases in their expression levels through virus-induced gene silencing (VIGS). Subsequently, the potential involvement of GhWRKY40 in the regulatory network was revealed: GhWRKY40 positively regulated GhAP3's expression according to transcriptional profiling, VIGS, yeast one-hybrid assays and dual-luciferase experiments. Furthermore, alterations in the expression of the eight previously reported cotton FL-responsive genes from the above three VIGS lines (GhAP3, GhAP4 and GhWRKY40) implied that MYB5_A12 was involved in the GhWRKY40-GhAP network. In short, we unveiled the unprecedented FL regulation roles of GhAPs in cotton, which was possibly further regulated by GhWRKY40. These findings will reveal the genetic basis of FL development associated with qFLD05 and be beneficial for the marker-assisted selection of long-staple cotton.

Map-based cloning of qLPA01.1, a favorable allele from the Gossypium tomentosum chromosome segment line

Cotton is an important natural fiber crop worldwide which plays a vital role in our daily life. High yield is a constant goal of cotton breeding, and lint percentage (LP) is one of the important components of cotton fiber yield. A stable QTL controlling LP, qLPA01.1, was identified on chromosome A01 from Gossypium hirsutum introgressed lines with G. tomentosum chromosome segments in a previous study. To fine-map qLPA01.1, an F2 population with 986 individuals was established by crossing G. hirsutum cultivar CCRI35 with the chromosome segment substitution line HT_390. A high-resolution genetic map including 47 loci and spanning 56.98 cM was constructed in the QTL region, and qLPA01.1 was ultimately mapped into an interval corresponding to an ~80 kb genome region of chromosome A01 in the reference genome, which contained six annotated genes. Transcriptome data and sequence analysis revealed that S-acyltransferase protein 24 (GoPAT24) might be the target gene of qLPA01.1. This result provides the basis for cotton fiber yield improvement via marker-assisted selection (MAS) and further studies on the mechanism of cotton fiber development.

Identification of QTLs associated with grain-filling duration and heading date in wheat.

An increase in genetic diversity of bread wheat caused by spring x winter forms leads to an alteration of genetic control of maturity time. Maturity time (MAT) is one of major yield components in wheat, which has two components: the heading date (HD) and grain-filling period (GFP). Using the Illumina Infinium 25k platform we analyzed the genetic control of the HD, GFP and MAT in the F2 and F2:3 populations from a cross between late-ripening spring/winter line 124-1 and spring wheat cultivar Novosibirskaya 31, possessing the same allelic composition of the VRN1 and PPD-D1 genes. The phenotypic evaluation of the populations studied was performed during three years. A total of 17 QTLs were mapped, out of which 4 QTLs for MAT or its components were confirmed over two years. Two common MAT and HD QTLs were identified on the 4A chromosome, and two loci controlling GFP and MAT were found on 6B chromosome. An environmentally stable HD QTL QHd.icg-7B.1 was associated with the FT-B1 gene having a non-synonymous polymorphism [G/C] in its coding region. A novel НD QTL was identified on 7D chromosome. QTL dissection allowed to propose putative genes for QMat.icg4-A and QMat.icg6-B, namely the SPL family gene (TraesCS4A02G359500) and the TCP transcription factor (TraesCS6B02G462100), respectively. The results of this study provide information for further investigation into wheat development.

Strawberry soluble solids QTL with inverse effects on yield.

Sugars are the main drivers of strawberry sweetness, and understanding their genetic control is of critical importance for breeding. Large-scale genome-wide association studies were performed in two populations totaling 3399 individuals evaluated for soluble solids content (SSC) and fruit yield. Two stable quantitative trait loci (QTL) on chromosome 3B and 6A for SSC were identified. Favorable haplotypes at both QTL for SSC decreased yield, though optimal allelic combinations were identified with reduced impacts on yield. Metabolites in the starch and sucrose metabolism pathway were characterized and quantified for 23 contrasting genotypes in leaves, white fruit, and red fruit. Variations in sucrose concentrations/efflux indicated genetic variation underlying sucrose accumulation and transportation during fruit ripening. Integration of genome-wide association studies and expression quantitative locus mapping identified starch synthase 4 (FxaC_10g00830) and sugar transporter 2-like candidate genes (FxaC_21g51570) within the respective QTL intervals. These results will enable immediate applications in genomics-assisted breeding for flavor and further study of candidate genes underlying genetic variation of sugar accumulation in strawberry fruit.

Identification of QTLs for plant height and branching related traits in cultivated peanut

Plant height (PH), primary lateral branch length (PBL) and branch number (BN) are architectural components impacting peanut pod yield, biomass production and adaptivity to mechanical harvesting. In this study, a recombinant inbred population consisting of 181 individual lines was used to determine genetic controls of PH, PBL and BN across three environments. Phenotypic data collected from the population demonstrated continuous distributions and transgressive segregation patterns. Broad-sense heritability of PH, PBL and BN was found to be 0.87, 0.88 and 0.92, respectively. Unconditional individual environmental analysis revealed 35 additive QTLs with phenotypic variation explained (PVE) ranging from 4.57 to 21.68%. A two-round meta-analysis resulted in 24 consensus and 17 unique QTLs. Five unique QTLs exhibited pleiotropic effects and their genetic bases (pleiotropy or tight linkage) were evaluated. Joint analysis was performed to estimate the QTL by environment interaction (QEI) effects on PH, PBL and BN, which collectively explained phenotypic variations of 10.80, 11.02, and 7.89%, respectively. We identified 3 major and stable QTL regions (uq9-3, uq10-2 and uq16-1) on chromosomes 9, 10 and 16, spanning 1.43-1.53 Mb genomic regions. Candidate genes involved in phytohormones biosynthesis, signaling and cell wall development were proposed to regulate these morphological traits. These results provide valuable information for further genetic studies and development of molecular markers applicable for peanut architecture improvement.

Identification and validation of major-effect quantitative trait locus QMS-5B associated with male sterility in photo-thermo-sensitive genic male sterile wheat.

QMS-5B, a major QTL for photo-thermo-sensitive genic male sterility in wheat, was fine mapped in a 2.15Mb region harboring a serine/threonine protein kinase gene TraesCS5B03G0887500, which was the most likely candidate gene. Genic male sterility is an essential trait in the utilization of heterosis and hybrid seed production for wheat. Currently, genic male sterile genes have been reported in wheat mutants, but the sterile genes controlling photo-thermo-sensitive genic male sterility in wheat have not been studied systematically. Here, 235 doubled haploid lines derived from a cross between photo-thermo-sensitive genic male sterile line BS462 and its restorer line CP279 were used to map male sterile gene by GenoBaits® Wheat 100K Panel, bulked segregant exome sequencing (BSE-Seq) and wheat 660K array. As a result, the major stable QTL on chromosome 5B, QMS-5B, was identified in all four environments, accounting for 7.3-36.4% of the phenotypic variances. Ulteriorly, QMS-5B was delimited to an approximate 2.15Mb physical interval between KASP-5B5 and KASP-5B6 using kompetitive allele-specific PCR (KASP) markers. Within the interval, twenty-nine high-confidence genes were predicted according to Chinese Spring RefSeq v2.1. TraesCS5B03G0887500, encoding a serine/threonine protein kinase, was identified as the most likely candidate gene for QMS-5B based on weighted gene co-expression network analysis. Expression analysis confirmed that TraesCS5B03G0887500 was significantly differentially expressed in anthers of BS462 and CP279 at different stages under fertile and sterile environments. In addition, flanking KASP marker KASP-5B6 can effectively genotype male sterile lines and restorer lines, and can be used for molecular marker-assisted selection. This study provides insights into for exploring the mechanism of photo-thermo-sensitive genic male sterility in wheat.

Molecular identification and validation of four stable QTL for adult-plant resistance to powdery mildew in Chinese wheat cultivar Bainong 64.

Four stable QTL for adult-plant resistance (APR) to powdery mildew were identified on chromosome arms 1DL, 2BS, 2DL, and 6BL in the widely grown Chinese wheat cultivar Bainong 64. These QTL had no effect on response to stripe rust or leaf rust. Wheat powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a devastating fungal disease. Seedlings of Chinese wheat Bainong 64 are susceptible to Bgt, but adult plants have maintained resistance since it was released in 1996. A population of 171 recombinant inbred lines (RILs) developed from cross Jingshuang 16/Bainong 64 (JS16/BN64) was used to dissect genetic components of powdery mildew resistance. A genetic map comprising 5383 polymorphic markers was constructed using the 15K SNP chip and kompetitive allele-specific PCR (KASP) markers. Composite interval mapping identified four stable QTL with favorable alleles all from BN64 on chromosome arms 1DL, 2BS, 2DL, and 6BL in at least four environments. They accounted for 8.3%, 13.8%, 14.4%, and 9.0% of the total phenotypic variation explained (PVE) in maximum, respectively. QPmjbr.caas-1DL, situated about 22Mb from centromere, is probably a new QTL. QPmjbr.caas-2DL located near the end of arm 2DL and explained the largest PVE. Using genetic maps populated with KASP markers, QPmjbr.caas-2BS and QPmjbr.caas-6BL were fine mapped to a 1.8cM genetic intervals spanning 13.6Mb (76.0-89.6Mb) and 1.7cM and 4.9Mb (659.9-664.8Mb), respectively. The four QTL independent of stripe rust and leaf rust resistance were validated for powdery mildew resistance in another RIL population related to BN64 and a cultivar panel using representative KASP markers. Since BN64 has been a leading cultivar and an important breeding parent in China, the QTL and markers reported in this study will be useful for marker-assisted selection of APR.

Molecular characterization of stable QTL and putative candidate genes for grain zinc and iron concentrations in two related wheat populations.

Major QTL for grain zinc and iron concentrations were identified on the long arm of chromosomes 2D and 6D. Gene-based KASP markers were developed for putative candidate genes TaIPK1-2D and TaNAS10-6D. Micronutrient malnutrition is one of the most common public health problems in the world. Biofortification, the most attractive and sustainable solution to surmount malnutrition requires the development of micronutrient enriched new crop cultivars. In this study, two recombinant inbred line (RIL) populations, ZM175/XY60 and ZM175/LX987, were used to identify QTL for grain zinc concentration (GZnC), grain iron concentration (GFeC) and thousand grain weight (TGW). Eight QTL for GZnC, six QTL for GFeC and five QTL for TGW were detected. Three QTL on chromosomes 2DL and 4BS and chromosome 6A showed pleiotropic effects on all three traits. The 4BS and 6A QTL also increased plant height and might be Rht-B1a and Rht25a, respectively. The 2DL locus within a suppressed recombination region was identified in both RIL populations and the favorable allele simultaneously increasing GZnC, GFeC and TGW was contributed by XY60 and LX987. A QTL on chromosome 6DL associated only with GZnC was detected in ZM175/XY60 and was validated in JD8/AK58 RILs using kompetitive allele-specific PCR (KASP) marker K_AX-110119937. Both the 2DL and 6DL QTL were new loci for GZnC. Based on gene annotations, sequence variations and expression profiles, thephytic acid biosynthesis gene TaIPK1-2D and nicotianamine synthase gene TaNAS10-6D were predicted as candidate genes. Their gene-based KASP markers were developed and validated in a cultivar panel of 343 wheat accessions. This study investigated the genetic basis of GZnC and GFeC and provided valuable candidate genes and markers for breeding Zn- and Fe-enriched wheat.

Slow stripe rusting in Chinese wheat Jimai 44 conferred by Yr29 in combination with a major QTL on chromosome arm 6AL.

YrJ44, a more effective slow rusting gene than Yr29, was localized to a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479 on chromosome 6AL. "Slow rusting" (SR) is a type of adult plant resistance (APR) that can provide non-specific durable resistance to stripe rust in wheat. Chinese elite wheat cultivar Jimai 44 (JM44) has maintained SR to stripe rust in China since its release despite exposure to a changing and variable pathogen population. An F2:6 population comprising 295 recombinant inbred lines (RILs) derived from a cross between JM44 and susceptible cultivar Jimai 229 (JM229) was used in genetic analysis of the SR. The RILs and parental lines were evaluated for stripe rust response in five field environments and genotyped using the Affymetrix Wheat55K SNP array and 13 allele-specific quantitative PCR-based (AQP) markers. Two stable QTL on chromosome arms 1BL and 6AL were identified by inclusive composite interval mapping. The 1BL QTL was probably the pleiotropic gene Lr46/Yr29/Sr58. QYr.nwafu-6AL (hereafter named YrJ44), mapped in a 3.5-cM interval between AQP markers AX-109373479 and AX-109563479, was more effective than Yr29 in reducing disease severity and relative area under the disease progress curve (rAUDPC). RILs harboring both YrJ44 and Yr29 displayed levels of SR equal to the resistant parent JM44. The AQP markers linked with YrJ44 were polymorphic and significantly correlated with stripe rust resistance in a panel of 1,019 wheat cultivars and breeding lines. These results suggested that adequate SR resistance can be obtained by combining YrJ44 and Yr29 and the AQP markers can be used in breeding for durable stripe rust resistance.

GmMFT: a potential step forward in soybean breeding for high oil and yield.

This article is a Commentary on Cai et al. (2023), 239: 905–919.