Genetic dissection of wheat panicle traits using linkage analysis and a genome-wide association study

Key message

Coincident regions on chromosome 4B for GW, on 5A for SD and TSS, and on 3A for SL and GNS were detected through an integration of a linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A and 6A were identified with high PVE% on a composite map.

Abstract

The panicle traits of wheat, such as grain number per spike and 1000-grain weight, are closely correlated with grain yield. Superior and effective alleles at loci related to panicles developments play a crucial role in the progress of molecular improvement in wheat yield breeding. Here, we revealed several notable allelic variations of seven panicle-related traits through an integration of genome-wide association mapping and a linkage analysis. The linkage analysis was performed using a recombinant inbred line (RIL) population (173 lines of F_8:9) with a high-density genetic map constructed with 90K SNP arrays, Diversity Arrays Technology (DArT) and simple sequence repeat (SSR) markers in five environments. Thirty-five additive quantitative trait loci (QTL) were discovered, including eleven stable QTLs on chromosomes 1A, 2D, 4B, 5B, 6B, and 6D. The marker interval between EX_C101685 and RAC875_C27536 on chromosome 4B exhibited pleiotropic effects for GW, SL, GNS, FSN, SSN, and TSS, with the phenotypic variation explained (PVE) ranging from 5.40 to 37.70%. In addition, an association analysis was conducted using a diverse panel of 205 elite wheat lines with a composite map (24,355 SNPs) based on the Illumina Infinium assay in four environments. A total of 73 significant marker-trait associations (MTAs) were detected for panicle traits, which were distributed across all wheat chromosomes except for 4D, 5D, and 6D. Consensus regions between RAC875_C27536_611 and Tdurum_contig4974_355 on chromosome 4B for GW in multiple environments, between QTSS5A.7-43 and BS00021805_51 on 5A for SD and TSS, and between QSD3A.2-164 and RAC875_c17479_359 on 3A for SL and GNS in multiple environments were detected through linkage analysis and a genome-wide association study (GWAS). In addition, six stable QTL clusters on chromosomes 2D, 3A, 4B, 5A, and 6A were identified with high PVE% on a composite map. This study provides potentially valuable information on the dissection of yield-component traits and valuable genetic alleles for molecular-design breeding or functional gene exploration.

     

Genetic analysis of shoot fresh weight in a cross of wild (<Emphasis Type="Italic">G. soja</Emphasis>) and cultivated (<Emphasis Type="Italic">G. max</Emphasis>) soybean

Shoot fresh weight (SFW) is one of the parameters, used to estimate the total plant biomass yield in soybean. In the present study, a total of 188 F_5:8 recombinant inbred lines (RIL) derived from an interspecific cross of PI 483463 (Glycine soja) and Hutcheson (Glycine max) were investigated for SFW variation in the field for three consecutive years. The parental lines and RILs were phenotyped in the field at the R6 stage by measuring total biomass in kg/plot to identify the QTLs for SFW. Three QTLs qSFW6_1, qSFW15_1, and qSFW19_1 influencing SFW were identified on chromosome 6, 15, and 19, respectively. The QTL qSFW19_1 flanked between the markers BARC-044913-08839 and BARC-029975-06765 was the stable QTL expressed in all the three environments. The phenotypic variation explained by the QTLs across all environments ranged from 6.56 to 21.32 %. The additive effects indicated contribution of alleles from both the parents and additive × environment interaction effects affected the expression of SFW QTL. Screening of the RIL population with additional SSRs from the qSFW19_1 region delimited the QTL between the markers SSR19-1329 and BARC-29975-06765. QTL mapping using bin map detected two QTLs, qSFW19_1A and qSFW19_1B. The QTL qSFW19_1A mapped close to the Dt1 gene locus, which affects stem termination, plant height, and floral initiation in soybean. Potential candidate genes for SFW were pinpointed, and sequence variations within their sequences were detected using high-quality whole-genome resequencing data. The findings in this study could be useful for understanding genetic basis of SFW in soybean.     

Identification and validation of quantitative trait loci controlling seed isoflavone content across multiple environments and backgrounds in soybean

Soybean is important throughout the world not only due to the high seed protein and oil but also owing to the seed isoflavone. To improve the isoflavone concentration in seeds, detecting and mining the stable and reliable quantitative trait loci (QTLs) and related genes in multiple environments and genetic backgrounds become more and more important. In view of this, a F_6:7 recombinant inbred line (RIL) population of 345 lines derived from a cross between Zheng 92116 and Liaodou14 (ZL) was genotyped using 1739 polymorphic SNP and 127 SSR markers in this study and was phenotyped for individual and total seed isoflavone in four environments over 2 years. In total, 48 additive QTLs, which explained 3.00–29.83% of seed isoflavone variation, were identified. Of them, eight QTLs (qDA1_1, qGA1_1, qTIA1_1, qDA1_2, qGA1_2, qTIA1_2, qDA1_3, qTIA1_3) with phenotypic variation explained (PVE) ranging from 14.09 to 28.59% for daidzin, genistin, and total isoflavone were located on the same region of linkage group (LG) A1. These QTLs were further verified in another RIL population derived from Zheng 92116 × Qihuang 30 (ZQ). Meanwhile, the other four overlapping QTLs on linkage group B1, which were associated with glycitin content (qGLB1_1, qGLB1_2, qGLB1_3, qGLB1_4) and explained 16.52 to 29.83% of phenotypic variation, were also verified using the ZQ population. Moreover, the individuals with different genotypes at the common flanking SNP markers for these QTLs on LGs A1 and B1 in the two mapping populations showed significant different isoflavone content, which further validate the QTL mapping results. And also, some candidate genes might participate in the isoflavone biosynthesis processes were found in these stable QTL regions. Thus, the novel and stable QTLs identified and verified in this study could be applied in marker-assisted selection breeding or map-based candidate genes cloning in soybean seed isoflavone genetic improvement in future.     

Mapping and validation of a new QTL for adult-plant resistance to powdery mildew in Chinese elite bread wheat line Zhou8425B

Key message

Four QTLs for adult-plant resistance to powdery mildew were mapped in the Zhou8425B/Chinese Spring population, and a new QTL on chromosome 3B was validated in 103 wheat cultivars derived from Zhou8425B.

Abstract

Zhou8425B is an elite wheat (Triticum aestivum L.) line widely used as a parent in Chinese wheat breeding programs. Identification of genes for adult-plant resistance (APR) to powdery mildew in Zhou8425B is of high importance for continued controlling the disease. In the current study, the high-density Illumina iSelect 90K single-nucleotide polymorphism (SNP) array was used to map quantitative trait loci (QTL) for APR to powdery mildew in 244 recombinant inbred lines derived from the cross Zhou8425B/Chinese Spring. Inclusive composite interval mapping identified QTL on chromosomes 1B, 3B, 4B, and 7D, designated as QPm.caas-1BL.1, QPm.caas-3BS, QPm.caas-4BL.2, and QPm.caas-7DS, respectively. Resistance alleles at the QPm.caas-1BL.1, QPm.caas-3BS, and QPm.caas-4BL.2 loci were contributed by Zhou8425B, whereas that at QPm.caas-7DS was from Chinese Spring. QPm.caas-3BS, likely to be a new APR gene for powdery mildew resistance, was detected in all four environments. One SNP marker closely linked to QPm.caas-3BS was transferred into a semi-thermal asymmetric reverse PCR (STARP) marker and tested on 103 commercial wheat cultivars derived from Zhou8425B. Cultivars with the resistance allele at the QPm.caas-3BS locus had averaged maximum disease severity reduced by 5.3%. This STARP marker can be used for marker-assisted selection in improvement of the level of powdery mildew resistance in wheat breeding.

     

Mapping of QTLs associated with resistance to common bunt,tan spot,leaf rust,and stripe rust in a spring wheat population

Spring wheat (Triticum aestivum L.) breeding goals in western Canada include good agronomic characteristics and good end-use quality, and also moderate to elevated resistance to diseases of economic importance. In this study, we aimed to identify quantitative trait loci (QTL) associated with resistance to common bunt (Tilletia tritici and Tilletia laevis), tan spot (Pyrenophora tritici-repentis), leaf rust (Puccinia triticina), and stripe rust (Puccinia striiformis f. sp. tritici). A total of 167 recombinant inbred lines (RILs) derived from a cross between two spring wheat cultivars, ‘Attila’ and ‘CDC Go’, were evaluated for reactions to the four diseases in nurseries from three to eight environments, and genotyped with the Wheat 90K SNP array and three gene-specific markers (Ppd-D1, Vrn-A1, and Rht-B1). The RILs exhibited transgressive segregation for all four diseases, and we observed several lines either superior or inferior to the parents. Broad-sense heritability varied from 0.25 for leaf rust to 0.48 for common bunt. Using a subset of 1203 informative markers (1200 SNPs and 3 gene-specific markers) and average disease scores across all environments, we identified two QTLs (QCbt.dms-1B.2 and QCbt.dms-3A) for common bunt, and three QTLs each for tan spot (QTs.dms-2B, QTs.dms-2D, and QTs.dms-6B), leaf rust (QLr.dms-2D.1, QLr.dms-2D.2, and QLr.dms-3A), and stripe rust (QYr.dms-3A, QYr.dms-4A, and QYr.dms-5B). Each QTL individually explained between 5.9 and 18.7% of the phenotypic variation, and altogether explained from 21.5 to 26.5% of phenotypic and from 52.2 to 86.0% of the genetic variation. The resistance alleles for all QTLs except one for stripe rust (QYr.dms-5B) were from CDC Go. Some of the QTLs are novel, while others mapped close to QTLs and/or genes reported in other studies.     

Contributions of <Emphasis Type="Italic">TaSUTs</Emphasis> to grain weight in wheat under drought

Key message

The homologous genes to OsSUT1-5 in wheat were identified and detailed analysed. TaSUT1 was the predominant sucrose transporter group and it illustrated the genotypic variations towards drought during grain filling.

Abstract

Sucrose transporters (SUT) play crucial roles in wheat stem water soluble carbohydrate (WSC) remobilization to grain. To determine the major functional SUT gene groups in shoot parts of wheat during grain development, drought tolerant varieties, Westonia and Kauz, were investigated in field drought experiments. Fourteen homologous genes to OsSUT1-5 were identified on five homeologous groups, namely TaSUT1_4A, TaSUT1_4B, TaSUT1_4D; TaSUT2_5A, TaSUT2_5B, TaSUT2_5D; TaSUT3_1A, TaSUT3_1D; TaSUT4_6A, TaSUT4_6B, TaSUT4_6D; TaSUT5_2A, TaSUT5_2B, and TaSUT5_2D, and their gene structures were analysed. Wheat plants above the ground were harvested from pre-anthesis to grain maturity and the stem, leaf sheath, rachis, lemma and developing grain were used for analysing TaSUT gene expression. Grain weight, thousand grain weight, kernel number per spike, biomass and stem WSC were characterized. The study showed that among the five TaSUT groups, TaSUT1 was the predominant sucrose transporting group in all organs sampled, and the expression was particularly high in the developing grain. In contrast to TaSUT1, the gene expression levels of TaSUT2, TaSUT3 and TaSUT4 were lower, except for TaSUT3 which showed preferential expression in the lemma before anthesis. The TaSUT5 gene group was very weakly expressed in all tissues. The upregulated gene expression of TaSUT1 Westonia type in stem and grain reveal a crucial role in stem WSC remobilization to grain under drought. The high TaSUT1 gene expression and the significant correlations with thousand grain weight (TGW) and kernel number per spike demonstrated the contribution in Kauz’s high grain yield in an irrigated environment and high TGW in Westonia under drought stress. Further molecular level identification is required for gene marker development.

     

Temperature-dependent QTLs in <Emphasis Type="Italic">indica</Emphasis> alleles for improving grain quality in rice: increased prominence of QTLs responsible for reduced chalkiness under high-temperature conditions

Quantitative trait loci (QTLs) for the apparent quality of brown rice under high temperatures during ripening were analyzed using chromosomal segment substitution lines. Segments from the indica cultivar Habataki were substituted into a japonica cultivar with a Sasanishiki background. We found the following two QTLs for increasing grain quality in the Habataki allele on chromosome 3: (1) qTW3-2, located near the marker RM14702, decreased the percentage of total white immature (TWI) grains, and (2) qRG3-2, located near RM3766, increased the percentage of regular grains. The effects of these two QTLs were more obvious under high-temperature ripening conditions; hence, these loci are considered QTLs not only for reducing TWI grains but also for increasing high-temperature tolerance. Additionally, we found two QTLs, i.e., qTW3-1 and qRG3-1, responsible for reduced grain quality near RM14314 on chromosome 3. Although the QTL for narrow grains in the Habataki allele qNG3 was genetically linked to qTW3-2, the effect was only slightly significant, and the length/width ratio of qNG3-carrying grains was within the range observed in widely grown japonica cultivars. Incorporating the Habataki region, including qRG3-2 and qTW3-2 but not qTW3-1 and qRG3-1, in addition to previously reported grain quality QTLs in breeding japonica cultivars will improve high-temperature tolerance and grain quality.     

A novel allele of <Emphasis Type="Italic">TaGW2</Emphasis>-<Emphasis Type="Italic">A1</Emphasis> is located in a finely mapped QTL that increases grain weight but decreases grain number in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Key message

A novel TaGW2-A1 allele was identified from a stable, robust QTL region, which is pleiotropic for thousand grain weight, grain number per spike, and grain morphometric parameters in wheat.

Abstract

Thousand grain weight (TGW) and grain number per spike (GNS) are two crucial determinants of wheat spike yield, and genetic dissection of their relationships can help to fine-tune these two components and maximize grain yield. By evaluating 191 recombinant inbred lines in 11 field trials, we identified five genomic regions on chromosomes 1B, 3A, 3B, 5B, or 7A that solely influenced either TGW or GNS, and a further region on chromosome 6A that concurrently affected TGW and GNS. The QTL of interest on chromosome 6A, which was flanked by wsnp_BE490604A_Ta_2_1 and wsnp_RFL_Contig1340_448996 and designated as QTgw/Gns.cau-6A, was finely mapped to a genetic interval shorter than 0.538 cM using near isogenic lines (NILs). The elite NILs of QTgw/Gns.cau-6A increased TGW by 8.33%, but decreased GNS by 3.05% in six field trials. Grain Weight 2 (TaGW2-A1), a well-characterized gene that negatively regulates TGW and grain width in wheat, was located within the finely mapped interval of QTgw/Gns.cau-6A. A novel and rare TaGW2-A1 allele with a 114-bp deletion in the 5′ flanking region was identified in the parent with higher TGW, and it reduced TaGW2-A1 promoter activity and expression. In conclusion, these results expand our knowledge of the genetic and molecular basis of TGW-GNS trade-offs in wheat. The QTLs and the novel TaGW2-A1 allele are likely useful for the development of cultivars with higher TGW and/or higher GNS.

     

QTL mapping of pre-harvest sprouting resistance in a white wheat cultivar Danby

Key message

One major and three minor QTLs for resistance to pre-harvest sprouting (PHS) were identified from a white wheat variety “Danby.” The major QTL on chromosome 3A is TaPHS1, and the sequence variation in its promoter region was responsible for the PHS resistance. Additive?×?additive effects were detected between two minor QTLs on chromosomes 3B and 5A, which can greatly enhance the PHS resistance.

Abstract

Pre-harvest sprouting (PHS) causes significant losses in yield and quality in wheat. White wheat is usually more susceptible to PHS than red wheat. Therefore, the use of none grain color-related PHS resistance quantitative trait loci (QTLs) is essential for the improvement in PHS resistance in white wheat. To identify PHS resistance QTLs in the white wheat cultivar “Danby” and determine their effects, a doubled haploid population derived from a cross of Danby?×?“Tiger” was genotyped using genotyping-by-sequencing markers and phenotyped for PHS resistance in two greenhouse and one field experiments. One major QTL corresponding to a previously cloned gene, TaPHS1, was consistently detected on the chromosome arm 3AS in all three experiments and explained 21.6–41.0% of the phenotypic variations. A SNP (SNP?222) in the promoter of TaPHS1 co-segregated with PHS in this mapping population and was also significantly associated with PHS in an association panel. Gene sequence comparison and gene expression analysis further confirmed that SNP?222 is most likely the causal mutation in TaPHS1 for PHS resistance in Danby in this study. In addition, two stable minor QTLs on chromosome arms 3BS and 5AL were detected in two experiments with allele effects consistently contributed by Danby, while one minor QTL on 2AS was detected in two environments with contradicted allelic effects. The two stable minor QTLs showed significant additive?×?additive effects. The results demonstrated that pyramiding those three QTLs using breeder-friendly KASP markers developed in this study could greatly improve PHS resistance in white wheat.

     

Genetic mapping and confirmation of quantitative trait loci for grain chalkiness in rice

Grain chalkiness is a highly undesirable trait affecting rice grain quality and milled rice yield. In order to clarify the genetic basis of chalkiness, a recombinant inbred line population (RIL) derived from a cross between Beilu130 (a japonica cultivar with high chalkiness) and Jin23B (an indica cultivar with low chalkiness) was developed for quantitative trait locus (QTL) mapping. A total of 10 QTLs for white belly rate (WBR) and white core rate (WCR) were detected on eight different chromosomes over 2 years. Two QTLs for WBR (qWBR2 and qWBR5) showed similar chromosomal locations with GW2 and qSW5/GW5, which have been cloned previously to control the grain width and should be the right candidate genes. Three novel minor QTLs controlling WCR, qWCR1, qWCR3, and qWCR4 were further validated in near isogenic F₂ populations (NIL-F₂) and explained 26.1, 18.3, and 21.1% of the phenotypic variation, respectively. These QTLs could be targets for map-based cloning of the candidate genes to elucidate the molecular mechanism of chalkiness and for marker-assisted selection (MAS) in rice grain quality improvement.     

Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat

Heading date is one of the most important traits in wheat breeding as it affects adaptation and yield potential. A genome-wide association study (GWAS) using the 90 K iSelect SNP genotyping assay indicated that a total of 306 loci were significantly associated with heading and flowering dates in 13 environments in Chinese common wheat from the Yellow and Huai wheat region. Of these, 105 loci were significantly correlated with both heading and flowering dates and were found in clusters on chromosomes 2, 5, 6, and 7. Based on differences in distribution of the vernalization and photoperiod genes among chromosomes, arms, or block regions, 13 novel, environmentally stable genetic loci were associated with heading and flowering dates, including RAC875_c41145_189 on 1DS, RAC875_c50422_299 on 2BL, and RAC875_c48703_148 on 2DS, that accounted for more than 20% phenotypic variance explained (PVE) of the heading/flowering date in at least four environments. GWAS and t test of a combination of SNPs and vernalization and photoperiod alleles indicated that the Vrn-B1, Vrn-D1, and Ppd-D1 genes significantly affect heading and flowering dates in Chinese common wheat. Based on the association of heading and flowering dates with the vernalization and photoperiod alleles at seven loci and three significant SNPs, optimal linear regression equations were established, which show that of the seven loci, the Ppd-D1 gene plays the most important role in modulating heading and flowering dates in Chinese wheat, followed by Vrn-B1 and Vrn-D1. Additionally, three novel genetic loci (RAC875_c41145_189, Excalibur_c60164_137, and RAC875_c50422_299) also show important effect on heading and flowering dates. Therefore, Ppd-D1, Vrn-B1, Vrn-D1, and the novel genetic loci should be further investigated in terms of improving heading and flowering dates in Chinese wheat. Further quantitative analysis of an F₁₀ recombinant inbred lines population identified a major QTL that controls heading and flowering dates within the Ppd-D1 locus with PVEs of 28.4% and 34.0%, respectively; this QTL was also significantly associated with spike length, peduncle length, fertile spikelets number, cold resistance, and tiller number.     

Molecular genetic analysis of grain protein content and flour whiteness degree using RILs in common wheat

Grain protein content (GPC) and flour whiteness degree (FWD) are important qualitative traits in common wheat. Quantitative trait locus (QTL) mapping for GPC and FWD was conducted using a set of 131 recombinant-inbred lines derived from the cross ‘Chuan 35050 × Shannong 483’ in six environmental conditions. A total of 22 putative QTLs (nine GPC and 13 FWD) were identified on 12 chromosomes with individual QTL explaining 4.5–34.0% phenotypic variation. Nine QTLs (40.9%) were detected in two or more environments. The colocated QTLs were on chromosomes 1B and 4B. Among the QTLs identified for GPC, QGpc.sdau-4A from the parent Shannong 483 represented some important favourable QTL alleles. QGpc.sdau-2A.1 and QFwd.sdau-2A.1 had a significant association with both GPC and FWD. The markers detected on top of QTL regions could be potential targets for marker-assisted selection.     

Genetic dissection of interactions between wheat flour starch and its components in two populations using two QTL mapping methods

Starch content and its components are important for determining wheat end-use quality and yield. However, little information is available about their interactions at the QTL/gene level in more than one population using different QTL mapping methods. Therefore, to dissect these interactions, two mapping populations from two locations over 2 years were used. The QTLs for the populations were analyzed by unconditional and conditional QTL mapping by two different analysis methods. In the two populations, there were a total of 24 unconditional additive QTLs detected for flour amylose (FAMS), flour amylopectin (FAMP), flour total starch (FTSC), and the ratio of FAMS to FAMP using ICIMapping4.1 methods, but 26 unconditional QTLs were found using QTLNetwork2.0 methods. Of these QTLs, 10 stable major additive QTLs were identified in more than one environment, mainly distributed on chromosomes 3B, 4A, 5A, and 7D. The maximum percentage of phenotypic variance explained (PVE) reached 54.31%. Two new unconditional major additive QTLs on chromosome 3B (Qftsc3B and Qfamp3B) were found. A total of 23 and 19 conditional additive QTLs were identified in the two populations using two different methods, respectively. Of which, eight and six stable major conditional QTLs were detected on chromosomes 3B, 4A, and 7D, respectively. New repressed QTLs were identified, such as Qftsc/fams5B-1 and Qftsc/fams5B-2. There were 20 epistatic unconditional and 15 conditional QTLs detected. In all, important QTLs on chromosomes 3B, 4A, and 7A were found in both populations. However, the number of important QTLs in the special recombinant inbred line (RIL) population was higher than that in the double haploid (DH) population, especially on chromosomes 7D and 5B. Moreover, the QTLs on chromosomes 4A, 7A, and 7D were close to the Wx-1 loci in the RIL population. These indicated better results can be obtained by a special population to target traits than by a common population. The important QTLs on key chromosomes can always be detected no matter what kinds of populations are used, such as the QTLs on chromosome 4A. In addition, QTL clusters were found on chromosomes 4A, 3B, 7A, 7D, and 5A in the two populations, indicating these chromosome regions were very important for starch biosynthesis.     

Genetic analysis and mapping of adult plant resistance loci to leaf rust in durum wheat cultivar Bairds

Key message

New leaf rust adult plant resistance (APR) QTL QLr.cim - 6BL was mapped and confirmed the known pleotropic APR gene Lr46 effect on leaf rust in durum wheat line Bairds.

Abstract

CIMMYT-derived durum wheat line Bairds displays an adequate level of adult plant resistance (APR) to leaf rust in Mexican field environments. A recombinant inbred line (RIL) population developed from a cross of Bairds with susceptible parent Atred#1 was phenotyped for leaf rust response at Ciudad Obregon, Mexico, during 2013, 2014, 2015 and 2016 under artificially created epidemics of Puccinia triticina (Pt) race BBG/BP. The RIL population and its parents were genotyped with the 50 K diversity arrays technology (DArT) sequence system and simple sequence repeat (SSR) markers. A genetic map comprising 1150 markers was used to map the resistance loci. Four significant quantitative trait loci (QTLs) were detected on chromosomes 1BL, 2BC (centromere region), 5BL and 6BL. These QTLs, named Lr46, QLr.cim-2BC, QLr.cim-5BL and QLr.cim-6BL, respectively, explained 13.5–60.8%, 9.0–14.3%, 2.8–13.9%, and 11.6–29.4%, respectively, of leaf rust severity variation by the inclusive composite interval mapping method. All of these resistance loci were contributed by the resistant parent Bairds, except for QLr.cim-2BC, which came from susceptible parent Atred#1. Among these, the QTL on chromosome 1BL was the known pleiotropic APR gene Lr46, whereas QLr.cim-6BL, a consistently detected locus, should be a new leaf rust resistance locus in durum wheat. The mean leaf rust severity of RILs carrying all four QTLs ranged from 8.0 to 17.5%, whereas it ranged from 10.9 to 38.5% for three QTLs (Lr46 + 5BL + 6BL) derived from the resistant parent Bairds. Two RILs with four QTLs combinations can be used as sources of complex APR in durum wheat breeding.

     

Genome-wide association studies provide insights on genetic architecture of resistance to leaf rust in a worldwide barley collection

We assembled an international barley panel comprising 282 entries from 26 countries with various levels of field resistance to leaf rust caused by Puccinia hordei. The panel was screened for leaf rust response with an array of pathotypes at the seedling stage, and at the adult plant stage in multiple environments (2013–2015) in Australia and Uruguay, and genotyped using >?13 K polymorphic DArT-Seq markers. Multipathotype testing in the greenhouse postulated the presence of seedling resistance genes Rph1, Rph2, Rph3, Rph4, Rph7, Rph9.am, Rph12, Rph14, Rph15, Rph19, and Rph25. Genome-wide association studies (GWAS) based on field data identified 13 QTLs significantly associated with DArT-Seq markers on chromosomes 2H (Rph_G_Q1, Rph_G_Q2, Rph_G_Q3, and Rph_G_Q4), 4H (Rph_G_Q5), 5H (Rph_G_Q6, Rph_G_Q7, Rph_G_Q8), 6H (Rph_G_Q9 and Rph_G_Q10), and 7H (Rph_G_Q11, Rph_G_Q12, and Rph_G_Q13). Three QTLs (Rph_G_Q3, Rph_G_Q5, and Rph_G_Q6) were detected under all environments, whereas the other ten were variable, being detected in 1–4 environments; Rph_G_Q1 and Rph_G_Q13 being detected only in Uruguay. Among the three QTLs detected under all environments, Rph_G_Q6 on chromosome 5H had the largest effect and corresponded to a region where the cataloged APR gene Rph20 is located. Rph_G_Q3 and Rph_G_Q5 detected on chromosome 2H and 4H aligned with QTLs reported in at least three previous studies. The studies provide useful information towards better understanding of the genetic architecture of seedling and adult plant resistance to leaf rust in diverse global barley germplasm.     

QTL mapping for yield and photosynthetic related traits under different water regimes in wheat

The improvement for drought tolerance requires understanding of the genetic control of wheat (Triticum aestivum L.) reaction to drought. In this study, a set of 131 recombinant inbred lines of wheat were investigated under well-watered (WW) and drought stress (DS) environments across 2 years to map quantitative trait loci (QTLs) for yield and physiological traits. A total of 225 QTLs were detected, including 32 non-environment-specific loci that were significant in both DS and WW, one drought-specific locus and two watering-specific loci. Three consistently-expressed QTLs (QTkw-3A.2, QTss-1A, and QScn-7A.1) were identified in at least three environments and the QTkw-1D.1 was significant in DS across the 2 years. By unconditional and conditional QTL analysis, spike number per plant and kernel number per spike were more important than thousand-kernel weight for grain yield (GY) at the given genetic background. Meta-analysis identified 67 meta-QTLs that contained QTLs for at least two traits. High frequency co-location of QTLs was found among either the spike-related traits or the six physiological traits. Four photosynthesis traits (CHL, LWUE, P _N, and C _i) were co-located with GY and/or yield components on various MQTLs. The results provided QTLs that warrant further study for drought tolerance breeding and are helpful for understanding the genetic basis of drought tolerance and the genetic contribution of yield components to GY at individual QTL level in wheat.     

Host plant quantitative trait loci affect specific behavioral sequences in oviposition by a stem-mining insect

Key message

Genetic diversity in quantitative loci associated with plant traits used by insects as cues for host selection can influence oviposition behavior and maternal choice.

Abstract

Host plant selection for oviposition is an important determinant of progeny performance and survival for phytophagous insects. Specific cues from the plant influence insect oviposition behavior; but, to date, no set of host plant quantitative trait loci (QTLs) have been shown to have an effect on behavioral sequences leading to oviposition. Three QTLs in wheat (Triticum aestivum L.) have been identified as influencing resistance to the wheat stem sawfly (WSS) (Cephus cinctus Norton). Wheat near-isogenic lines (NILs) for each of the three QTLs were used to test whether foraging WSS were able to discriminate variation in plant cues resulting from allelic changes. A QTL on chromosome 3B (Qss-msub-3BL) previously associated with stem solidness and larval antibiosis was shown to affect WSS oviposition behavior, host preference, and field infestation. Decreased preference for oviposition was also related to a QTL allele on chromosome 2D (Qwss.msub-2D). A QTL on chromosome 4A (Qwss.msub-4A.1) affected host plant attractiveness to foraging females, but did not change oviposition preference after females landed on the stem. These findings show that oviposition decisions regarding potential plant hosts require WSS females to discriminate signals from the plant associated with allelic variation at host plant quantitative loci. Allele types in a host plant QTL associated with differential survival of immature progeny can affect maternal choices for oviposition. The multidisciplinary approach used here may lead to the identification of plant genes with important community consequences, and may complement the use of antibiosis due to solid stems to control the wheat stem sawfly in agroecosystems.

     

QTL mapping of mandarin (<Emphasis Type="Italic">Citrus reticulata</Emphasis>) fruit characters using high-throughput SNP markers

Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F₁ population derived from ‘Fortune’ × ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (Citrus clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. A cluster of QTLs for flavedo color space values L, a, b, and a/b and juice color space values a and a/b were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.     

Identification of candidate genes of QTLs for seed weight in <Emphasis Type="Italic">Brassica napus</Emphasis> through comparative mapping among <Emphasis Type="Italic">Arabidopsis</Emphasis> and <Emphasis Type="Italic">Brassica</Emphasis>species

Background

Map-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare.

Results

In this study, a whole genome genetic linkage map for B. napus was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus.

Conclusions

Our study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance.

     

Interactions between <Emphasis Type="Italic">Glu-1</Emphasis> and <Emphasis Type="Italic">Glu-3</Emphasis> loci and associations of selected molecular markers with quality traits in winter wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.) DH lines

The quality of wheat depends on a large complex of genes and environmental factors. The objective of this study was to identify quantitative trait loci controlling technological quality traits and their stability across environments, and to assess the impact of interaction between alleles at loci Glu-1 and Glu-3 on grain quality. DH lines were evaluated in field experiments over a period of 4 years, and genotyped using simple sequence repeat markers. Lines were analysed for grain yield (GY), thousand grain weight (TGW), protein content (PC), starch content (SC), wet gluten content (WG), Zeleny sedimentation value (ZS), alveograph parameter W (APW), hectolitre weight (HW), and grain hardness (GH). A number of QTLs for these traits were identified in all chromosome groups. The Glu-D1 locus influenced TGW, PC, SC, WG, ZS, APW, GH, while locus Glu-B1 affected only PC, ZS, and WG. Most important marker-trait associations were found on chromosomes 1D and 5D. Significant effects of interaction between Glu-1 and Glu-3 loci on technological properties were recorded, and in all types of this interaction positive effects of Glu-D1 locus on grain quality were observed, whereas effects of Glu-B1 locus depended on alleles at Glu-3 loci. Effects of Glu-A3 and Glu-D3 loci per se were not significant, while their interaction with alleles present at other loci encoding HMW and LMW were important. These results indicate that selection of wheat genotypes with predicted good bread-making properties should be based on the allelic composition both in Glu-1 and Glu-3 loci, and confirm the predominant effect of Glu-D1d allele on technological properties of wheat grains.