Stable QTL Research Articles

Leaf thickness of barley: genetic dissection, candidate genes prediction and its relationship with yield-related traits.

In this first genetic study on assessing leaf thickness directly in cereals, major and environmentally stable QTL were detected in barley and candidate genes underlying a major locus were identified. Leaf thickness (LT) is an important characteristic affecting leaf functions which have been intensively studied. However, as LT has a small dimension in many plant species and technically difficult to measure, previous studies on this characteristic are often based on indirect estimations. In the first study of detecting QTL controlling LT by directly measuring the characteristic in barley, large and stable loci were detected from both field and glasshouse trials conducted in different cropping seasons by assessing a population of 201 recombinant inbred lines. Four loci (locating on chromosome arms 2H, 3H, 5H and 6H, respectively) were consistently detected for flag leaf thickness (FLT) in each of these trials. The one on 6H had the largest effect, with a maximum LOD 9.8 explaining up to 20.9% of phenotypic variance. FLT does not only show strong interactions with flag leaf width and flag leaf area but has also strong correlations with fertile tiller number, spike row types, kernel number per spike and heading date. Though with reduced efficiency, these loci were also detectable from assessing second last leaf of fully grown plants or even from assessing the third leaves of seedlings. Taking advantage of the high-quality genome assemblies for both parents of the mapping population used in this study, three candidate genes underlying the 6H QTL were predicted based on orthologous analysis. These results do not only broaden our understanding on genetic basis of LT and its relationship with other traits in cereal crops but also form the bases for cloning and functional analysis of genes regulating LT in barley.

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat.

Bread wheat is a highly adaptable food crop grown extensively around the world and its quality genetic improvement has received wide attention. In this study, the genetic loci associated with five quality traits including protein content (PC), gluten content (GC), baking value (BV), grain hardness (HA), and sedimentation value (SV) in a population of 253 Chinese wheat grown in Inner Mongolia were investigated through genome wide association mapping. A total of 103 QTL containing 556 SNPs were significantly related to the five quality traits based on the phenotypic data collected from three environments and BLUP data. Of these QTL, 32 QTL were continuously detected under at least two experiments. Some QTL such as qBV3D.2/qHA3D.2 on 3D, qPC5A.3/qGC5A on 5A, qBV5D/qHA5D on 5D, qBV6B.2/qHA6B.3 on 6B, and qBV6D/qHA6D.1 on 6D were associated with multiple traits. In addition, distribution of favorable alleles of the stable QTL in the association panel and their effects on five quality traits were validated. Analysis of existing transcriptome data revealed that 34 genes were specifically highly expressed in grains during reproductive growth stages. The functions of these genes will be characterized in future experiments. This study provides novel insights into the genetic basis of quality traits in wheat.

TIP41L, a putative candidate gene conferring both seed size and boll weight, was fine-mapped in an introgression line of Gossypium hirsutum-Gossypium arboreum

QTLs for yield-related traits in tetraploid cotton have been widely mapped, but QTLs introduced from diploid species into tetraploid cotton background remain uninvolved. Here, a stable introgression line with the traits of small boll and seed on Chr. A12, IL197 derived from Gossypium hirsutum (2n = AADD = 52) × Gossypium arboreum (2n = AA = 26), was employed to construct the F2 and F3 secondary populations for fine-mapping QTLs of yield-related traits. QTL analysis showed eight QTLs were detected for three traits, boll weight (BW), seed index (SI, one-hundred-seed weight in g), and lint percentage, with 3.94–28.13 % of the phenotypic variance explained. Of them, a stable major QTL, q(BW + SI)-A12-1 controlling both BW and SI and covering the shortest region in Chr. A12, was further narrowed into a 60.09 kb-interval through substitution mapping. Finally, five candidate genes were detected in the interval. The qRT-PCR analysis revealed only TIP41-like family protein (TIP41L) kept up-regulated expression and significantly lower in TM-1 than that in IL197 from -1 DPA to 15 DPA during cotton boll rapid developmental stage. Therefore, TIP41L gene is speculated as the most likely candidate gene. Comparative analysis with the other four allotetraploid species showed TIP41L gene was probably diverged after the formation of allotetraploid cotton, which may be selected and swept during domestication of modern upland cotton because small boll and seed are detrimental to fibre yield of cotton. This research would lay a solid foundation for further elucidating the molecular mechanism of cotton boll and seed development.

Stable QTL for malate levels in ripe fruit and their transferability across Vitis species.

Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%), and based on two and five years of data, respectively, their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.

Identification and Fine-Mapping of a Novel QTL, qMrdd2, That Confers Resistance to Maize Rough Dwarf Disease.

Maize rough dwarf disease (MRDD) is caused by a virus and seriously affects maize quality and yield worldwide. MRDD can be most effectively controlled with disease-resistant hybrids of corn. Here, MRDD-resistant (Qi319) and -susceptible (Ye478) parental inbred maize lines and their 314 recombinant inbred lines (RILs) that were derived from a cross between them were evaluated across three environments. A stable resistance QTL, qMrdd2, was identified and mapped using best linear unbiased prediction (BLUP) values to a 0.55-Mb region between the markers MK807 and MK811 on chromosome 2 (B73 RefGen_v3) and was found to explain 8.6 to 11.0% of the total phenotypic variance in MRDD resistance. We validated the effect of qMrdd2 using a chromosome segment substitution line (CSSL) that was derived from a cross between maize inbred Qi319 as the MRDD resistance donor and Ye478 as the recipient. Disease severity index of the CSSL haplotype II harboring qMrdd2 was significantly lower than that of the susceptible parent Ye478. Subsequently, we fine-mapped qMrdd2 to a 315-kb region flanked by the markers RD81 and RD87, thus testing recombinant-derived progeny using selfed backcrossed families. In this study, we identified a novel QTL for MRDD resistance by combining the RIL and CSSL populations, thus providing important genetic information that can be used for breeding MRDD-resistant varieties of maize.

Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship.

The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.

Identification of novel QTL contributing to barley yellow mosaic resistance in wild barley (Hordeum vulgare spp. spontaneum)

BackgroundBarley yellow mosaic disease (BYMD) caused by Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV) seriously threatens the production of winter barley. Cultivating and promoting varieties that carry disease-resistant genes is one of the most powerful ways to minimize the disease’s effect on yield. However, as the BYMD virus mutates rapidly, resistance conferred by the two cloned R genes to the virus had been overcome by new virus strains. There is an urgent need for novel resistance genes in barley that convey sustainable resistance to newly emerging virus strains causing BYMD.ResultsA doubled haploid (DH) population derived from a cross of SRY01 (BYMD resistant wild barley) and Gairdner (BYMD susceptible barley cultivar) was used to explore for QTL of resistance to BYMD in barley. A total of six quantitative trait loci (qRYM-1H, qRYM-2Ha, qRYM-2Hb, qRYM-3H, qRYM-5H, and qRYM-7H) related to BYMD resistance were detected, which were located on chromosomes 1H, 2H, 3H, 5H, and 7H. Both qRYM-1H and qRYM-2Ha were detected in all environments. qRYM-1H was found to be overlapped with rym7, a known R gene to the disease, whereas qRYM-2Ha is a novel QTL on chromosome 2H originated from SRY01, explaining phenotypic variation from 9.8 to 17.8%. The closely linked InDel markers for qRYM-2Ha were developed which could be used for marker-assisted selection in barley breeding. qRYM-2Hb and qRYM-3H were stable QTL for specific resistance to Yancheng and Yangzhou virus strains, respectively. qRYM-5H and qRYM-7H identified in Yangzhou were originated from Gairdner.ConclusionsOur work is focusing on a virus disease (barley yellow mosaic) of barley. It is the first report on BYMD-resistant QTL from wild barley accessions. One novel major QTL (qRYM-2Ha) for the resistance was detected. The consistently detected new genes will potentially serve as novel sources for achieving pre-breeding barley materials with resistance to BYMD.

Mapping stem rust resistance loci effective in Kenya in Canadian spring wheat (Triticum aestivum L.) lines ‘AAC Prevail’ and ‘BW961’

This study was conducted to identify and map stem rust resistance genes in Canada Western Red Spring (CWRS) wheat variety ‘AAC Prevail’ and elite line ‘BW961ʹ. A population of 227 doubled haploid lines from ‘AAC Prevail’/‘BW961ʹ and parents were evaluated for their response to stem rust (Puccinia graminis) at Njoro, Kenya, from 2016–2019 and genotyped using a targeted genotyping by sequencing SeqSNP assay. ‘AAC Prevail’ and ‘BW961ʹ were susceptible to race TTKSK in seedling tests in Canada. We identified stable QTL (significant in most environments tested) associated with field stem rust resistance on chromosome arms 2BS and 7AL, and minor QTL on 5AL, 6AS and 7BL. The QTL on 5AL, 7AL and 7BL were contributed by ‘AAC Prevail’, while those on 2BS and 6AS were contributed by ‘BW961ʹ. The QTL on 7AL was detected across all environments and explained 9.5% to 39% of the variation in disease severity (DS) and infection response (IR). The QTL on 2BS was associated with DS in all environments and in three of four environments for IR, and explained 4.8% to 12% of the variation in DS and IR. In two environments, the combination of 2BS and 7AL significantly enhanced field stem rust resistance compared with either QTL singly. Using SNP markers closely linked to the novel QTL on 2BS and 7AL, Kompetitive Allele Specific PCR markers were developed and validated in the population. These results provide breeders with new information and markers to utilize these sources of stem rust resistance.

Identification of safflower (Carthamus tinctorius L.) QTL under drought stress and normal conditions

As a potential oil producer, safflower (Carthamus tinctorius L.) is advisable for growing in marginal and dry areas. The scarcity of identified linked markers is a major restriction to successful breeding programs in safflower for unfavorable environments. The genetic enhancement of safflower is a prerequisite to improve its utility and acceptability as an oilseed crop. Thus, this study aimed to determine QTL monitoring the importance and determination of epistatic impacts and QTL inter loci interaction as well as QTL by interaction in the F9 population derived from a Mex 22-191/Goldasht safflower under normal and drought stress conditions in the growing season of 2019. A new linkage map with 69 polymorphic AFLP markers was made which covered 556 cM of the safflower genome. At last, 17 major QTL with additive impacts (A) and 66 epistatic QTL with additive × additive impacts (AA) for ten agronomic traits in different environments were determined. The additive and epistatic QTL described 3.04%-24.71% and 8.31%-56.5 %–24.71 % and 8.31 %–56.5 % of the phenotypic variations of traits, respectively. Seven main genomic regions on linkage group (LG) 4 and LG5 were co-localized QTL for various traits. QTL by interactions found that four additive QTL were included in AE, and ten epistatic QTL were involved in AAE impacts, indicating that stress vis-à-vis non-stress conditions responsible for QTL. The identity linked markers with main and stable QTL can be applied as information markers for future investigations to introduce the candidate markers for breeding programs in safflower to increase the effectiveness of selection or drought tolerance enhancement.

QTL Genetic Mapping Study for Traits Affecting Meal Quality in Winter Oilseed Rape (Brassica Napus L.).

Rapeseed (Brassica napus L.) meal is an important source of protein, but the presence of anti-nutritional compounds, such as fibre and glucosinolates, still limits its use as a livestock feed. Understanding the genetic basis of seed fibre biosynthesis would help to manipulate its content in seeds of oilseed rape. Here, we applied high-resolution skim genotyping by sequencing (SkimGBS) and characterised 187,835 single-nucleotide polymorphism (SNP) markers across a mapping population subsequently used for a genetic mapping study (R/qtl). This approach allowed the identification of 11 stable QTL related to seed quality traits and led to the identification of potential functional genes underlying these traits. Among these, key genes with a known role in carbohydrate metabolic process, cell wall, lignin, and flavonoid biosynthesis, including cellulase GH5, TT10/LAC15, TT4, and SUC2, were found. This study furthers the understanding of the molecular mechanisms underlying seed fibre content and provides new markers for molecular breeding in B. napus.

QTL mapping for starch paste viscosity of rice (Oryza sativa L.) using chromosome segment substitution lines derived from two sequenced cultivars with the same Wx allele

BackgroundThe eating and cooking qualities (ECQs) of rice (Oryza sativa L.) are key characteristics affecting variety adoption and market value. Starch viscosity profiles tested by a rapid visco analyzer (RVA) offer a direct measure of ECQs and represent the changes in viscosity associated with starch gelatinization. RVA profiles of rice are controlled by a complex genetic system and are also affected by the environment. Although Waxy (Wx) is the major gene controlling amylose content (AC) and ECQs, there are still other unknown genetic factors that affect ECQs.ResultsQuantitative trait loci (QTLs) for starch paste viscosity in rice were analyzed using chromosome segment substitution lines (CSSLs) developed from the two cultivars 9311 and Nipponbare, which have same Wx-b allele. Thus, the effect of the major locus Wx was eliminated and the other locus associated with the RVA profile could be identified. QTLs for seven parameters of the starch RVA profile were tested over four years in Nanjing, China. A total of 310 QTLs were identified (from 1 to 55 QTLs per trait) and 136 QTLs were identified in more than one year. Among them, 6 QTLs were stalely detected in four years and 26 QTLs were detected in at least three years including 13 pleiotropic loci, controlling 2 to 6 RVA properties simultaneously. These stable QTL hotspots were co-located with several known starch synthesis-related genes (SSRGs). Sequence alignments showed that nucleotide and amino acid sequences of most SSRGs were different between the two parents. Finally, we detected stable QTLs associated with multiple starch viscosity traits near Wx itself, supporting the notion that additional QTLs near Wx control multiple characteristic values of starch viscosity.ConclusionsBy eliminating the contribution from the major locus Wx, multiple QTLs associated with the RVA profile of rice were identified, several of which were stably detected over four years. The complexity of the genetic basis of rice starch viscosity traits might be due to their pleiotropic effects and the multiple QTL hot spots. Minor QTLs controlling starch viscosity traits were identified by using the chromosome segment substitution strategy. Allele polymorphism might be the reason that QTLs controlling RVA profile characteristics were detected in some known SSRG regions.

Fine mapping and validation of a major QTL for grain weight on chromosome 5B in bread wheat.

A major QTL QTgw.caas-5B for thousand grain weight in wheat was fine mapped on chromosome 5B, and TraesCS5B02G044800 was predicted to be the candidate gene. Thousand grain weight (TGW), determined by grain length and width, and is an important yield component in wheat; understanding of the underlying genes and molecular mechanisms remains limited. A stable QTL QTgw.caas-5B for TGW was identified previously in a RIL population developed from a cross between Zhongmai 871 (ZM871) and a sister line Zhongmai 895 (ZM895), and the aim of this study was to perform fine mapping and validate the genetic effect of the QTL. It was delimited to an interval of approximately 2.0Mb flanked by markers Kasp_5B29 and Kasp_5B31 (49.6-51.6Mb) using 12 heterozygous recombinant plants obtained by selfing a residual BC1F6 line selected from the ZM871/ZM895//ZM871 population. A candidate gene was predicted following sequencing and differential expression analyses. Marker Kasp_5B_Tgw based on a SNP in TraesCS5B02G044800, the QTgw.caas-5B candidate, was developed and validated in a diversity panel of 166 cultivars. The precise mapping of QTgw.caas-5B laid a foundation for cloning of a predicted causal gene and provides a molecular marker for improving grain yield in wheat.

Meta-analysis of genome-wide association studies reveal common loci controlling agronomic and quality traits in a wide range of normal and heat stressed environments.

Several stable QTL were detected using metaGWAS analysis for different agronomic and quality traits under 26 normal and heat stressed environments. Heat stress, exacerbated by global warming, has a negative influence on wheat production worldwide and climate resilient cultivars can help mitigate these impacts. Selection decisions should therefore depend on multi-environment experiments representing a range of temperatures at critical stages of development. Here, we applied a meta-genome wide association analysis (metaGWAS) approach to detect stable QTL with significant effects across multiple environments. The metaGWAS was applied to 11 traits scored in 26 trials that were sown at optimal or late times of sowing (TOS1 and TOS2, respectively) at five locations. A total of 2571 unique wheat genotypes (13,959 genotypes across all environments) were included and the analysis conducted on TOS1, TOS2 and both times of sowing combined (TOS1&2). The germplasm was genotyped using a 90k Infinium chip and imputed to exome sequence level, resulting in 341,195 single nucleotide polymorphisms (SNPs). The average accuracy across all imputed SNPs was high (92.4%). The three metaGWAS analyses revealed 107 QTL for the 11 traits, of which 16 were detected in all three analyses and 23 were detected in TOS1&2 only. The remaining QTL were detected in either TOS1 or TOS2 with or without TOS1&2, reflecting the complex interactions between the environments and the detected QTL. Eight QTL were associated with grain yield and seven with multiple traits. The identified QTL provide an important resource for gene enrichment and fine mapping to further understand the mechanisms of gene × environment interaction under both heat stressed and unstressed conditions.

QTL mapping of root traits in wheat under different phosphorus levels using hydroponic culture

BackgroundPhosphorus (P) is an important in ensuring plant morphogenesis and grain quality, therefore an efficient root system is crucial for P-uptake. Identification of useful loci for root morphological and P uptake related traits at seedling stage is important for wheat breeding. The aims of this study were to evaluate phenotypic diversity of Yangmai 16/Zhongmai 895 derived doubled haploid (DH) population for root system architecture (RSA) and biomass related traits (BRT) in different P treatments at seedling stage using hydroponic culture, and to identify QTL using 660 K SNP array based high-density genetic map.ResultsAll traits showed significant variations among the DH lines with high heritabilities (0.76 to 0.91) and high correlations (r = 0.59 to 0.98) among all traits. Inclusive composite interval mapping (ICIM) identified 34 QTL with 4.64–20.41% of the phenotypic variances individually, and the log of odds (LOD) values ranging from 2.59 to 10.43. Seven QTL clusters (C1 to C7) were mapped on chromosomes 3DL, 4BS, 4DS, 6BL, 7AS, 7AL and 7BL, cluster C5 on chromosome 7AS (AX-109955164 - AX-109445593) with pleiotropic effect played key role in modulating root length (RL), root tips number (RTN) and root surface area (ROSA) under low P condition, with the favorable allele from Zhongmai 895.ConclusionsThis study carried out an imaging pipeline-based rapid phenotyping of RSA and BRT traits in hydroponic culture. It is an efficient approach for screening of large populations under different nutrient conditions. Four QTL on chromosomes 6BL (2) and 7AL (2) identified in low P treatment showed positive additive effects contributed by Zhongmai 895, indicating that Zhongmai 895 could be used as parent for P-deficient breeding. The most stable QTL QRRS.caas-4DS for ratio of root to shoot dry weight (RRS) harbored the stable genetic region with high phenotypic effect, and QTL clusters on 7A might be used for speedy selection of genotypes for P-uptake. SNPs closely linked to QTLs and clusters could be used to improve nutrient-use efficiency.

QTL underlying iron toxicity tolerance at seedling stage in backcross recombinant inbred lines (BRILs) population of rice using high density genetic map

Fe is a trace element considered to be essential for rice, and it drives several metabolic processes. Fe toxicity occurs due to excessive Fe ions (Fe2+) and which, disturb cellular homeostasis and dramatically reduces the rice yield. A set of 118 BRILs made from a cross of japonica cv.’02428’ and indica ‘Changhui 891’ was used with high density bin map constructed by using high quality SNP to identify the QTL for Fe toxicity tolerance. As a whole total of 23 QTL were identified for various seedling traits, 3 under control with phenotypic difference ranging from 14.21% to 62.46%, 11 QTL under stress with phenotypic difference ranging from 7.89% to 47.39% and 9 under stressed/control ratio with phenotypic variance ranging from 9.17% to 183.50%. LOD values of QTL ranging from 4.05 to 17.04 in control, 3.41 to 8.09 in stress and 2.84 to131.63 in stress/control ratio. Shoot length (SL), root length (RL), shoot fresh weight (SFW), root fresh weight (RFW), shoot dry weight (SDW), and root dry weight (RDW), were used to estimate the degree of Fe tolerance. Many stable QTL, qSSDW-4, qSSDW-6, qRSDW-4 and qRSDW-6 affecting SDW were detected and beside this some new QTL, qRSFW-1, qRRFW-10 and qRRDW-1 were successfully identified significantly contributing to Fe toxicity tolerance in rice. The results of current study indicated that these novel regions could be transferred via markers assisted section and QTL pyramiding to develop Fe resistant lines in rice.

Identification of Promising RILs for High Grain Zinc Through Genotype × Environment Analysis and Stable Grain Zinc QTL Using SSRs and SNPs in Rice (Oryza sativa L.).

Polished rice is one of the commonly consumed staple foods across the world. However, it contains limited nutrients especially iron (Fe) and zinc (Zn). To identify promising recombinant inbred lines (RILs) for grain Zn and single plant yield, 190 RILs developed from PR116 and Ranbir Basmati were evaluated in two environments (E1 and E2). A subset of 44 contrasting RILs for grain Zn was screened in another two environments (E3 and E4). Phenotypic data was collected for 10 traits, viz., days to 50% flowering, plant height, panicle length, number of tillers, single plant yield (SPY), test weight, Fe and Zn in brown (IBR, ZBR), and polished rice (IPR, ZPR). Stepwise regression analysis of trait data in 190 RILs and a subset of 44 RILs revealed the interdependence of ZPR, ZBR, IPR, and IBR and the negative association of grain Zn with single plant yield. Based on the additive main effect and multiplicative interaction (AMMI) and genotype and genotype × environment interaction (GGE) analyses of the subset of 44 RILs across four environments (E1–E4), six promising RILs were identified for ZPR with >28 ppm. Mapping of 190 RILs with 102 simple sequence repeats (SSRs) resulted in 13 QTLs for best linear unbiased estimates (BLUEs) of traits including advantage over check (AOC). Using genotype-based sequencing (GBS), the subset of 44 RILs was mapped with 1035 single-nucleotide polymorphisms (SNPs) and 21 QTLs were identified. More than 100 epistatic interactions were observed. A major QTL qZPR.1.1 (PV 37.84%) and another QTL qZPR.11.1 (PV 15.47%) were identified for grain Zn in polished rice. A common major QTL (qZBR.2.1 and qZPR.2.1) was also identified on chromosome 2 for grain Zn content across SSR and SNP maps. Two potential candidate genes related to transporters were identified based on network analyses in the genomic regions of QTL < 3 Mb. The RILs identified for grain Zn and SPY were nominated for national evaluation as under rice biofortification, and two QTLs identified based on BLUEs could be used in the rice biofortification breeding programs.

Mapping of Ug99 stem rust resistance in Canadian durum wheat

Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), has potential to cause major yield losses in durum wheat. Development of durum cultivars with improved resistance to stem rust is a sustainable option for effective control of this disease. This study was conducted to identify genomic regions associated with resistance to Ug99-derived Pgt races using a doubled haploid (DH) mapping population produced from a cross between the resistant experimental line A9919-BY5C and the moderately susceptible cultivar ‘Strongfield’. The parents and DH lines were phenotyped for adult plant disease severity and infection response at Njoro, Kenya, for four years, and for seedling reaction to race TTKSK in a containment facility near Morden, Canada. Composite interval mapping using 612 SNP and DArT markers indicated four significant QTL for resistance to stem rust on chromosomes 1B, 4A, 5B, and 6A. A major and stable QTL from A9919-BY5C was identified on the short arm of chromosome 6A (6AS), which accounted for 71% of variation explained for seedling resistance and up to 46% for field resistance. This QTL mapped near the Sr8 locus and may be Sr8155B1, or a novel gene at the same location. Another QTL for adult plant resistance from A9919-BY5C was mapped on chromosome 1B that explained up to 14% of the phenotypic variation and likely is Sr14. Two minor QTL were identified in ‘Strongfield’ on chromosomes 4A and 5B that were inconsistent over years. Markers associated with the 6AS and 1B QTL can be used to proactively stack resistance to Ug99-derived races of Pgt into Canadian durum wheat.

QTL controlling fiber quality traits under salt stress in upland cotton (Gossypium hirsutum L.)

Key messageQTL for fiber quality traits under salt stress discerned candidate genes controlling fatty acid metabolism.Salinity stress seriously affects plant growth and limits agricultural productivity of crop plants. To dissect the genetic basis of response to salinity stress, a recombinant inbred line population was developed to compare fiber quality in upland cotton (Gossypium hirsutum L.) under salt stress and normal conditions. Based on three datasets of (1) salt stress, (2) normal growth, and (3) the difference value between salt stress and normal conditions, 51, 70, and 53 QTL were mapped, respectively. Three QTL for fiber length (FL) (qFL-Chr1-1, qFL-Chr5-5, and qFL-Chr24-4) were detected under both salt and normal conditions and explained 4.26%, 9.38%, and 3.87% of average phenotypic variation, respectively. Seven genes within intervals of two stable QTL (qFL-Chr1-1 and qFL-Chr5-5) were highly expressed in lines with extreme long fiber. A total of 35 QTL clusters comprised of 107 QTL were located on 18 chromosomes and exhibited pleiotropic effects. Thereinto, two clusters were responsible for improving five fiber quality traits, and 6 influenced FL and fiber strength (FS). The QTL with positive effect for fiber length exhibited active effects on fatty acid synthesis and elongation, but the ones with negative effect played passive roles on fatty acid degradation under salt stress.

Multi-parent QTL mapping reveals stable QTL conferring resistance to Gibberella ear rot in maize

Maize production is on risk by Gibberella ear rot (GER) caused by Fusarium graminearum. This is one of the most important ear rot diseases in temperate zones as it leads to yield losses and production of harmful mycotoxins. We investigated, for the first time, the potential use of Brazilian tropical maize to increase resistance levels to GER in temperate European flint germplasm by analyzing six interconnected biparental populations. We assessed GER symptoms in Brazil and in Europe in up to six environments (= location × year combinations) during the growing seasons of 2018 and 2019. We conducted multi-parent QTL and biparental QTL mapping, and identified four QTLs with additive gene action, each explaining 5.4 to 21.8% of the total genotypic variance for GER resistance. Among them, QTL q1 was stable across test environments, populations, and between inbred lines and testcrosses. The accuracies of genomic prediction ranged from 0.50 to 0.59 depending on the resistance donor and prediction model. Jointly, our study reveals the potential use of Brazilian resistance sources to increase GER resistance levels by genomics-assisted breeding.

QTL detection and putative candidate gene prediction for leaf rolling under moisture stress condition in wheat

Leaf rolling is an important mechanism to mitigate the effects of moisture stress in several plant species. In the present study, a set of 92 wheat recombinant inbred lines derived from the cross between NI5439 × HD2012 were used to identify QTLs associated with leaf rolling under moisture stress condition. Linkage map was constructed using Axiom 35 K Breeder’s SNP Array and microsatellite (SSR) markers. A linkage map with 3661 markers comprising 3589 SNP and 72 SSR markers spanning 22,275.01 cM in length across 21 wheat chromosomes was constructed. QTL analysis for leaf rolling trait under moisture stress condition revealed 12 QTLs on chromosomes 1B, 2A, 2B, 2D, 3A, 4A, 4B, 5D, and 6B. A stable QTL Qlr.nhv-5D.2 was identified on 5D chromosome flanked by SNP marker interval AX-94892575–AX-95124447 (5D:338665301–5D:410952987). Genetic and physical map integration in the confidence intervals of Qlr.nhv-5D.2 revealed 14 putative candidate genes for drought tolerance which was narrowed down to six genes based on in-silico analysis. Comparative study of leaf rolling genes in rice viz., NRL1, OsZHD1, Roc5, and OsHB3 on wheat genome revealed five genes on chromosome 5D. Out of the identified genes, TraesCS5D02G253100 falls exactly in the QTL Qlr.nhv-5D.2 interval and showed 96.9% identity with OsZHD1. Two genes similar to OsHB3 viz. TraesCS5D02G052300 and TraesCS5D02G385300 exhibiting 85.6% and 91.8% identity; one gene TraesCS5D02G320600 having 83.9% identity with Roc5 gene; and one gene TraesCS5D02G102600 showing 100% identity with NRL1 gene were also identified, however, these genes are located outside Qlr.nhv-5D.2 interval. Hence, TraesCS5D02G253100 could be the best potential candidate gene for leaf rolling and can be utilized for improving drought tolerance in wheat.