Wheat Recombinant Inbred Lines Research Articles

Diversity in bread and durum wheat stigma morphology and linkage of increased stigma length to dwarfing gene Rht14

Key messageThe dwarfing allele Rht14 of durum wheat associates with greater stigma length, an important trait for hybrid breeding, whilst major dwarfing alleles Rht-B1b and Rht-D1b showed little to no effect.Although much understudied in wheat, the stigma is a crucial component for attaining grain set, the fundamental basis for yield, particularly in hybrid production systems where successful grain set relies on wind-driven pollen dispersal by the male parent and effective pollen capture by the female parent. Females with long stigma that exsert early are thought to be advantageous. Using glasshouse-grown lines, we examined variation in Total Stigma Length (TSL) across diverse panels comprising 27 durum and 116 bread wheat genotypes. Contrasting genotypes were selected for population development and genetic analysis. Quantitative trait loci (QTL) analysis was performed on a durum F2 population and a bread wheat recombinant inbred line (RIL) population. Contrasting with studies of anther length, we found no large effect on TSL of the GA-insensitive semi-dwarfing genes Rht-B1 and Rht-D1 in either durum or bread wheat. However, in durum cultivar Italo, we identified a region on chromosome 6A which is robustly associated with larger TSL and contains the Rht14 allele for reduced plant height, a trait that is favourable for female line development in hybrid systems. This dual effect locus explained 25.2 and 19.2% of TSL phenotypic variation in experiments across two growing seasons, with preliminary results suggesting this locus may increase TSL when transferred to bread wheat. In a bread wheat, RIL population minor QTL on 1A and 2A was indicated, but the strongest association was with Ppd-B1. Methods developed here, and the identification of a TSL-enhancing locus provides advances and further opportunities in the study of wheat stigma.

Unlocking genetic insights: Evaluating wheat RILs for physiobiochemical traits under terminal heat stress conditions

BackgroundThe increasing impacts of heat stress on wheat production due to climate change has entailed the development of heat-resilient crop varieties. To address this, two hundred recombinant inbred lines (RILs) derived from a cross between WH711/WH1021 were evaluated in a randomized block design (RBD) with two replications at CCSHAU, Hisar, during 2018-19 under heat stress and non-stress conditions. Heat stress was induced by altering the date of sowing so that the grain filling stage coincide with heat stress.ResultsHeat stress adversely affects RILs performance, as illustrated by alterations in phenotypic traits. Highest coefficients of variations were recorded for TAA, CTD 1, WUE, CTD 2, Cc and A under non-stress and heat stress conditions whereas gs, WUEi and GY under non-stress and SPAD 1, SPAD 2, GY and NDVI 2 under heat-stress conditions recorded moderate estimates of coefficient of variations. CTD 2, TAA, E, WUE and A displayed a significant occurrence of both high heritability and substantial genetic advance under non-stress. Similarly, CTD 2, NDVI 2, A, WUEi, SPAD 2, gs, E, Ci, MDA and WUE exhibited high heritability with high genetic advance under heat-stress conditions.ConclusionsComplementary and duplicate types of interactions with number of controlling genes were observed for different parameters depending on the traits and environments. RILs 41, 42, 59, 74, 75, 180 and 194 were categorized as heat tolerant RILs. Selection preferably for NDVI 1, RWC, TAA, A, E and WUEi to accumulate heat tolerance favorable alleles in the selected RILs is suggested for development of heat resilient genotypes for sustainable crop improvement. The results showed that traits such as such as NDVI, RWC, TAA, A, E, and WUEi, can be effective for developing heat-resilient wheat genotypes and ensuring sustainable crop improvement.

Associations between allelic differences of the fifth group chromosome loci and a complex of agronomically valuable traits in common wheat (Triticum aestivum L.)

Aim. Characterization of recombinant inbred wheat lines by agronomically relevant traits and detection of asso- ciations between their expression level and allelic differences of microsatellite loci of the fifth group chromosomes. Methods. Phenological observations, morphometric indicators, and elements of crop structure. Statistical analysis of the obtained data was carried out in Microsoft Excel. The significance of the difference between samples was assessed by Fisher’s F test. A difference of p < 0.05 was considered statistically significant for all indicators. Results. The poly- morphism of the parental genotypes and the population of 47 recombinant-inbred lines (RILs) F7 from the crossing of the winter wheat varieties Luzanivka odeska and Odeska chervonokolosa over three years (2016–2018) in conditions of the Southern Steppe (Odesa) was evaluated according to eight characteristics: duration of a period prior to heading, plant height, productive tillering, grain number per spike, grain weight per spike, thousand-grain weight, productive tiller number per unit area and grain yield. The comparison of the data of line evaluation by agronomic traits against the data of microsatellite analysis of lines by 14 microsatellite loci of the fifth group chromosomes demonstrated the associations between several loci and grain yield and between two loci and plant height. Conclusions. The changes in grain yield in the most unfavorable year, 2018, were associated with allelic differences of lines at locus Xbarc319- 5A, and in the most favorable year, 2017, – with another locus of chromosome 5A, Xbarc330-5A. In both cases, the lines that had an allele from Odeska chervonokolosa were characterized by a significantly higher level of grain yield compared to the lines that had an allele from the Luzanivka odeska variety. There are at least two QTLs on 5B chromo- some, associated with winter wheat grain yield in favorable growing years. The first of them is located in the region of locus Xbarc88-5B, and the second – in the region of loci Xwmc415-5B, Xgpw3191-5B, and Xcfd7-5B. Based on the alleles of the specified microsatellite loci, which are linked QTLs of grain yield, it is possible to select genotypes at the early stages of selection that will give a higher yield in years with favorable conditions for growing wheat.

Low-temperature acclimation related with developmental regulations of polyamines and ethylene metabolism in wheat recombinant inbred lines

Winter survival is determined by complicated developmental regulations enabling wheat to adjust their transcriptome and metabolome to develop low temperature (LT) tolerance. The aim of the study was to clarify the metabolic responses developmentally regulated in six F6 recombinant inbred lines from a cross between Pishtaz (spring parent) and Mironovskaya 808 (winter parent). Spring genotypes, including pishtaz, RILs 4006 and 4014 showed lower LT tolerance, PAs (except the spermin), GABA and proline contents and DPPH• scavenging capacity. In these genotypes, genes and enzymes involved in the pathways of PAs and GABA degradation and ethylene biosynthesis were more active than other genotypes. RILs 4012 and 4016 with short vernalization displayed higher tolerance and lower H2O2 content compared to Pishtaz. Strong vernalization requirements in winter and facultative genotypes (Mironovskaya 808 parent and RILs 4003 and 4005) results in up-regulation of the metabolites and genes involved in PAs and GABA biosynthesis pathways (particularly when vernalization fulfillment occurred) to establish high tolerance as compared to genotypes without vernalization requirement. LT tolerance in all genotypes significantly decreased after vernalization fulfillment in February. Results indicated that LT tolerance was partly validated from developmental regulation of PAs, GABA, and ethylene metabolism during venalization and LT acclimation.

Holistic approach to ascertain genetic variability and responsive trait selection for different heat regimes of central India via field screening of wheat recombinant inbred lines

AbstractHigh temperature affects wheat yield severely. This study aimed to explore the variation and recognition of heat responsive traits, to enhance wheat productivity in high temperature stress condition. The recombinant inbred lines were developed by crossing of released wheat variety MACS2496 (heat sensitive) and WH730 (heat tolerant). The experiments were conducted into 2 years at three locations of two planting conditions (heat and terminal heat stress). Combined analysis of variance shows significant variations among all the studied traits at individual location, year and planting conditions. The phenological and yield component traits were highly influenced by environment under terminal heat stress condition. Days to heading and thousand kernel weight coupled with high heritability and high genetic advance per cent of mean in heat and terminal heat stress environments. In heat and terminal heat stress planting conditions, tiller number per plant, kernels per spike, kernel weight per spike and thousand kernel weight confirm positive relationship with grain yield per plant by correlation and principal component analysis. Path and multiple regression analysis accomplish that tiller number per plant, kernel weight per spike, kernel per spike and thousand kernel weight were identified as the key contributor towards grain yield per plant in heat and terminal heat stress environment. Thus, all‐inclusive approaches demonstrated that the promising traits deliver a framework to develop heat tolerant cultivars in future.

Genetic insight of recombinant inbred lines of wheat for Karnal bunt resistance using bulk segregant analysis

Genetic insight of recombinant inbred lines of wheat for Karnal bunt resistance using bulk segregant analysis

Mapping QTLs Controlling Grain and Leaf Traits in Iranian Wheat Recombinant Inbred Lines

Mapping QTLs Controlling Grain and Leaf Traits in Iranian Wheat Recombinant Inbred Lines

Nitrogen uptake and remobilization from pre- and post-anthesis stages contribute towards grain yield and grain protein concentration in wheat grown in limited nitrogen conditions

BackgroundIn wheat, nitrogen (N) remobilization from vegetative tissues to developing grains largely depends on genetic and environmental factors. The evaluation of genetic potential of crops under limited resource inputs such as limited N supply would provide an opportunity to identify N-efficient lines with improved N utilisation efficiency and yield potential. We assessed the genetic variation in wheat recombinant inbred lines (RILs) for uptake, partitioning, and remobilization of N towards grain, its association with grain protein concentration (GPC) and grain yield.MethodsWe used the nested association mapping (NAM) population (195 lines) derived by crossing Paragon (P) with CIMMYT core germplasm (P × Cim), Baj (P × Baj), Watkins (P × Wat), and Wyalkatchem (P × Wya). These lines were evaluated in the field for two seasons under limited N supply. The plant sampling was done at anthesis and physiological maturity stages. Various physiological traits were recorded and total N uptake and other N related indices were calculated. The grain protein deviation (GPD) was calculated from the regression of grain yield on GPC. These lines were grouped into different clusters by hierarchical cluster analysis based on grain yield and N-remobilization efficiency (NRE).ResultsThe genetic variation in accumulation of biomass at both pre- and post-anthesis stages were correlated with grain-yield. The NRE significantly correlated with aboveground N uptake at anthesis (AGNa) and grain yield but negatively associated with AGN at post-anthesis (AGNpa) suggesting higher N uptake till anthesis favours high N remobilization during grain filling. Hierarchical cluster analysis of these RILs based on NRE and yield resulted in four clusters, efficient (31), moderately efficient (59), moderately inefficient (58), and inefficient (47). In the N-efficient lines, AGNa contributed to 77% of total N accumulated in grains, while it was 63% in N-inefficient lines. Several N-efficient lines also exhibited positive grain protein deviation (GPD), combining high grain yield and GPC. Among crosses, the P × Cim were superior and N-efficient, while P × Wya responded poorly to low N input.ConclusionsWe propose that traits favouring pre- or post-anthesis biomass accumulation and pre-anthesis N uptake may be targeted for breeding to improve grain-yield under limited N. The lines with positive GPD, a first report of genotype-dependent GPD associated with both AGNpa and AGNa in wheat, may be used as varieties or genetic resources to improve grain yield with high GPC for sustainable development under limited N conditions.

Mapping Quantitative Trait Loci for Type II Fusarium Head Blight Resistance in Two Wheat Recombinant Inbred Line Populations Derived from Yangmai 4 and Yangmai 5.

Fusarium head blight (FHB) is a destructive wheat disease worldwide and significantly affects grain yield and quality in wheat. To understand the genetic basis underlying type II FHB resistance in two elite wheat cultivars Yangmai 4 (YM4) and Yangmai 5 (YM5), quantitative trait loci (QTL) mapping was conducted in two recombinant inbred lines (RIL) populations derived from the crosses of YM4 and YM5 with susceptible cultivar Yanzhan 1 (YZ1), respectively. Survey with markers linked to Fhb1, Fhb2, Fhb4, and Fhb5 in landrace Wangshuibai indicated the non-existence of these known FHB resistance genes/QTL in YM4, YM5, and YZ1. One overlapped resistance QTL was identified in both RIL populations, namely QFhb.Y4.2D/QFhb.Y5.2D, with a large effect on FHB resistance. One novel resistance QTL QFhb.Y4.5A mapped on chromosome 5A was detected only in YM4/YZ1 population. The resistance alleles of both QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A did not increase the plant height and did not significantly affect the heading date and flowering date. Kompetitive Allele-Specific PCR markers for QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A had been developed to verify in an additional set of 244 geographically diverse cultivars/lines. Pyramiding of the two resistance alleles decreased the percentage of symptomatic spikelets by 51.77% relative to the cultivars/lines without these two resistance alleles. QFhb.Y4.2D/QFhb.Y5.2D and QFhb.Y4.5A were shown to be useful alternatives in FHB resistance breeding programs. The results will facilitate the marker-assisted selection for introgression of the favorable alleles for improving FHB resistance in breeding programs.

A pleiotropic QTL increased economic water use efficiency in bread wheat (Triticum aestivum L.).

Wheat is one of the most important food crops in the world and drought can severely impact on wheat productivity. The identification and deployment of genes for improved water use efficiency (WUE) can help alleviate yield loss under water limitation. In this study, a high-density genetic linkage map of wheat recombinant inbred lines (Ningchun 4 x Ningchun 27) containing 8751 specific locus amplified fragment (SLAF) tags (including 14757 SNPs), with a total map distance of 1685 cM and an average inter-marker map distance of 0.19 cM was constructed by SLAF-seq technology. The economic yield WUE and nine related traits under three water treatments was monitored over four years. The results showed that loci conditioning WUE were also associated with grain carbon isotope discrimination (CID), flag leaf chlorophyll content, plant height, 1000-grain weight, grain weight per spike and grain number per spike. One locus on chromosome 2B explained 26.3% WUE variation in multiple environments. Under good soil moisture conditions before flowering, the high CID genotype QWue.acn-2B Ningchun 27, was associated with WUE, high grain weight per spike, and kilo-grain weight. Under rain-fed conditions, the low CID genotype QWue.acn-2B Ningchun 4 tended to maintain more spike number and was associated with improved WUE and yield. The introduction of good chromosome fragments of QWue.acn-2B into elite lines by molecular marker assisted selection will boost up the cultivation of high-yield and water-saving wheat varieties.

AMMI analysis for grain yield in bread wheat recombinant inbred lines

Identification of high yielding relatively stable genotypes is an integral objective of plant breeding programs. Testing of genotypes across environments is required to determine yield stability of genotypes. The specific objective of the current study was to analyze genotype by environment interaction (GEI) for grain yield of 44 bread wheat recombinant inbred lines (RILs) and six check cultivars using additive main effect and multiplicative interaction (AMMI) model. Experiments were planted using alpha lattice design with two replicates in Peshawar (E-1 and E-3), Hangu (E-2 and E-4) and Kohat (E-5) Khyber Pakhtunkhwa province, Pakistan. Analysis of variance revealed significant differences among RILs for all traits while interactions due to genotype by environment were significant for all traits except days to emergence and 1000-grain weight. Significant GEI justified environment-specific as well as AMMI analysis to identify RILs with specific and wider adaptation. The AMMI analysis revealed that the first interaction principal component analysis (IPCA 1) captured 64% of GEI sum of squares while the second interaction principal component analysis (IPCA 2) explained 25.8% of the interaction sum of square. The AMMI biplot identified G30 as high yielding genotype followed by G19 and G49, whereas low yielding RILs were G13, G8 and G7. Similarly G30, being close to IPCA1 axis, was the most stable RIL with wider adaptability followed by G31 and G25. Based on AMMI stability value (ASV), RILs G18 (2.15), G5 (2.78), G27 (3.72), G44 (4.31), G25 (4.43), G42 (4.57), G43 (5.78), G11 (5.82), G1 (7.66) and G29 (7.81) were recognized in the given order of relative stability. Stability analysis identified G49 (Wafaq ? Ghaznavi-98-3) as high yielding stable genotype among RILs which can be commercialized after fulfilling procedural requirements.

Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis.

Although wheat (Triticum aestivum L.) is the main staple crop in the world and a major source of carbohydrates and proteins, functional genomics and allele mining are still big challenges. Given the advances in next-generation sequencing (NGS) technologies, the identification of causal variants associated with a target phenotype has become feasible. For these reasons, here, by combining sequence capture and target-enrichment methods with high-throughput NGS re-sequencing, we were able to scan at exome-wide level 46 randomly selected bread wheat individuals from a recombinant inbred line population and to identify and classify a large number of single nucleotide polymorphisms (SNPs). For technical validation of results, eight randomly selected SNPs were converted into Kompetitive Allele-Specific PCR (KASP) markers. This resource was established as an accessible and reusable molecular toolkit for allele data mining. The dataset we are making available could be exploited for novel studies on bread wheat genetics and as a foundation for starting breeding programs aimed at improving different key agronomic traits.

QTL mapping of seedling and field resistance to stem rust in DAKIYE/Reichenbachii durum wheat population.

Stem rust caused by the fungus Puccinia graminis f.sp. tritici Eriks. & E. Henn. (Pgt) threatens the global production of both durum wheat (Triticum turgidum L. ssp. durum (Desf.) Husnot) and common wheat (Triticum aestivum L.). The objective of this study was to evaluate a durum wheat recombinant inbred line (RIL) population from a cross between a susceptible parent 'DAKIYE' and a resistant parent 'Reichenbachii' developed by the International Center for the Improvement of Maize and Wheat (CIMMYT) 1) for seedling response to races JRCQC and TTRTF and 2) for field response to a bulk of the current Pgt races prevalent in Ethiopia and Kenya and 3) to map loci associated with seedling and field resistances in this population. A total of 224 RILs along with their parents were evaluated at the seedling stage in the Ethiopian Institute for Agricultural Research greenhouse at Debre Zeit, Ethiopia and in the EIAR and KALRO fields in Ethiopia and Kenya, for two seasons from 2019 to 2020. The lines were genotyped using the genotyping-by-sequencing approach. A total of 843 single nucleotide polymorphism markers for 175 lines were used for quantitative trait locus (QTL) analyses. Composite interval mapping (CIM) identified three QTL on chromosomes 3B, 4B and 7B contributed by the resistant parent. The QTL on chromosome 3B was identified at all growth stages and it explained 11.8%, 6.5%, 6.4% and 15.3% of the phenotypic variation for responses to races JRCQC, TTRTF and in the field trials ETMS19 and KNMS19, respectively. The power to identify additional QTL in this population was limited by the number of high-quality markers, since several markers with segregation distortion were eliminated. A cytological study is needed to understand the presence of chromosomal rearrangements. Future evaluations of additional durum lines and RIL families identification of durable adult plant resistance sources is crucial for breeding stem rust resistance in durum wheat in the future.

Identification of carriers of Puccinia striiformis resistance genes in the population of recombinant inbred wheat lines

Stripe rust (yellow rust) caused by Puccinia striiformis f. sp. tritici, one of the most dangerous diseases of wheat. Marker assisted selection methods make it possible to accelerate the selection of resistance gene donors to improve breeding material through their introduction into hybridization programs. The goal of this study was to determine the presence/absence of yellow rust resistance genes in wheat recombinant inbred lines Almaly/Avocet (S) and to evaluate their response to Pst. Evaluation of seedling resistance to Pst allowed us to select 2 lines simultaneously resistant to races 111Е231 and 7E63. Race 7E63 was avirulent to most samples, and 111Е231 was highly virulent. All the studied lines demonstrated a resistant and moderately resistant reaction to the causative agent of yellow rust at the adult plant stage (R-MR). Molecular screening revealed the presence of a marker allele associated with the Yr18/Lr34 gene complex in 5 RIL. The frequency of resistant genotypes inheriting the Yr18 gene was 22.7%. The results can be used in MAS wheat breeding programs to increase resistance to yellow rust of wheat.

Two QTL for kernel number per spike identified from durum wheat

As one of the three yield components, kernel number per spike (KNPS) plays a key role in determining wheat yield. In this study, in combination with the previously constructed genetic map for a tetraploid wheat recombinant inbred line (RIL) population developed from the cross between a durum wheat and a wild emmer wheat and phenotype data from four environments, two major and stably expressed quantitative trait loci (QTL) for KNPS were identified. The phenotypic variation explained by these two QTL, Qknps-DW-3A.1 and Qknps-DW-3A.2, was up to 12.52% and 29.52%, respectively. The positive alleles were both from the durum wheat. Pyramiding analysis suggested that the combination of these two positive alleles has the largest effect on increasing KNPS. Comparison of physical interval for these two QTL with those reported previously showed that they may be novel loci. Genetic correlations between KNPS and other agronomic traits were also evaluated. Taken together, the two major and stably expressed QTL for KNPS from tetraploid wheat reported here they should be useful in wheat breeding. Supplemental data for this article is available online at https://doi.org/10.1080/13102818.2022.2054728 .

Spike Density Quantitative Trait Loci Detection and Analysis in Tetraploid and Hexaploid Wheat Recombinant Inbred Line Populations.

Spike density (SD) is an agronomically important character in wheat. In addition, an optimized spike structure is a key basis for high yields. Identification of quantitative trait loci (QTL) for SD has provided a genetic basis for constructing ideal spike morphologies in wheat. In this study, two recombinant inbred line (RIL) populations (tetraploid RIL AM and hexaploid RIL 20828/SY95-71 (2SY)) previously genotyped using the wheat55K SNP array were used to identify SD QTL. A total of 18 QTL were detected, and three were major and one was stably expressed (QSd.sau-2SY-7A.2, QSd.sau-AM-5A.2, QSd.sau-AM-7B, and QSd.sau-2SY-2D). They can explain up to 23.14, 19.97, 12.00, and 9.44% of phenotypic variation, respectively. QTL × environment and epistatic interactions for SD were further analyzed. In addition, pyramiding analysis further revealed that there were additive effects between QSd.sau-2SY-2D and QSd.sau-2SY-7A.2 in 2SY, and QSd.sau-AM-5A.2 and QSd.sau-AM-7B in AM. Pearson’s correlation between SD and other agronomic traits, and effects of major or stable QTL on yield related traits indicated SD significantly impacted spike length (SL), spikelet number per spike (SNS) and kernel length (KL). Several genes related to spike development within the physical intervals of major or stable QTL were predicted and discussed. Collectively, our research identified QTL with potential applications for modern wheat breeding and broadening the genetic basis of SD.

Chlorophyll Fluorescence and Drought Tolerance in a Mapping Population of Durum Wheat

Summary This study was conducted to compare and estimate the genetic variability among durum wheat lines in response to drought according to their grain yields and physiological traits. The use of fluorescence parameters as drought selection criteria for durum wheat was investigated in a population of 249 recombinant inbred lines (RILs) derived from a cross between two cultivars of durum wheat: ‘Svevo’ and ‘Kofa’. The durum wheat RILs considered were analyzed to determine the relationship between their grain yields and chlorophyll fluorescence parameters at the grain filling stage under drought stress (rainfed) and supplemental irrigation (irrigated) conditions during the 2004 and 2005 seasons at the ICARDA center. The results obtained show that the durum wheat line performance was influenced by drought stress, indicating significant differences between the grain yields and fluorescence parameters recorded under drought rainfed (RF) and irrigation (IR) conditions. Significant differences between the experimental groups of durum wheat RILs (P<0.05) were only recorded under drought conditions, with the exception of leaf water potential (Lwp). Under such conditions, nearly all the parameters examined were significantly increased in the high-yielding group (with the exception of the Que parameter), thus revealing the genetic variability of the durum wheat lines considered in response to drought stress. The potential quantum efficiency of photosystem II (Fv/Fm) was found to be positively associated with the grain yield parameter. The mean values of Fv/Fm in both the high- and low-yielding groups significantly dropped under drought stress (0.71 and 0.68, respectively) compared to the Fv/Fm values recorded under irrigated conditions (0.80 and 0.81). Under drought conditions, slopes were highly significant (P<0.001) nearly for all the fluorescence parameters examined (with the exception of CHLSPAD) compared to those recorded under irrigation conditions. It was concluded that chlorophyll content (SPAD), F0, Fm, Fv, Fv/Fm, Lwp, and Que could be used as additional indicators in screening wheat germplasm for drought tolerance.

Registration of the Coda/Brundage wheat recombinant inbred line mapping population

AbstractA mapping population (Reg. no. MP‐15, NSL 540708 MAP) composed of a cross between the soft white common winter wheat (Triticum aestivum L. subsp. aestivum) ‘Brundage’ (PI 599193) and the soft white club winter wheat (T. aestivum L. subsp. compactum) ‘Coda’ (PI 594372) was developed to maximize diversity within the soft white market class. The population comprises 268 F6:7 lines developed through single seed descent. The genetic linkage map consists of 2,144 DNA markers and is assigned to 32 linkage groups covering all chromosomes except 1D. This population was initially developed to determine additional markers linked to the Pch1 gene in wheat. It has further been used to identify quantitative trait loci (QTL) associated with resistance to other diseases such as Cephalosporium stripe (caused by Cephalosporium gramineum) and stripe rust (caused by Puccinia striiformis Westend. f. sp. tritici Erikss). The mapping population has also been used for identification of DNA markers associated with freezing tolerance, end‐use quality, and the compactum locus. From the differences in traits between the parental lines, the Coda/Brundage population provides the opportunity for further inquiry into the genes behind the identified QTL. The parents have only been phenotypically screened for a limited number of traits, and further screening may identify more polymorphic traits which the population can be used to map. It can also serve as a validation population for marker‐trait associations identified in other populations or other genetic studies such as recombination frequency.

Genetic dissection of wheat uppermost-internode diameter and its association with agronomic traits in five recombinant inbred line populations at various field environments

Uppermost-internode diameter (UID) is a key morphological trait associated with spike development and yield potential in wheat. Our understanding of its genetic basis remains largely unknown. Here, quantitative trait loci (QTLs) for UID with high-density genetic maps were identified in five wheat recombinant inbred line (RIL) populations. In total, 25 QTLs for UID were detected in five RIL populations, and they were located on chromosomes 1A, 1D (3 QTL), 2B (2), 2D (3), 3B, 3D, 4A, 4B (3), 4D, 5A (5), 5B (2), 6B, and 7D. Of them, five major and stable QTLs (QUid.sau-2CN-1D.1, QUid.sau-2SY-1D, QUid.sau-QZ-2D, QUid.sau-SC-3D, and QUid.sau-AS-4B) were identified from each of the five RIL populations in multiple environments. QUid.sau-2CN-1D.1, QUid.sau-2SY-1D and QUid.sau-SC-3D are novel QTLs. Kompetitive Allele Specific PCR (KASP) markers tightly linked to them were further investigated for developing near-isogenic lines (NILs) carrying the major loci. Furthermore, candidate genes at these intervals harboring major and stable QTLs were predicted, and they were associated with plant development and water transportation in most cases. Comparison of physical locations of the identified QTL on the ‘Chinese Spring’ reference genome showed that several QTLs including two major ones, QUid.sau-2CN-1D.1 and QUid.sau-2SY-1D, are likely allelic confirming their validity and effectiveness. The significant relationships detected between UID and other agronomic traits and a proper UID were discussed. Collectively, our results dissected the underlying genetic basis for UID in wheat and laid a foundation for further fine mapping and map-based cloning of these QTLs.

The 55K SNP-Based Exploration of QTLs for Spikelet Number Per Spike in a Tetraploid Wheat (Triticum turgidum L.) Population: Chinese Landrace "Ailanmai" × Wild Emmer.

Spikelet number per spike (SNS) is the primary factor that determines wheat yield. Common wheat breeding reduces the genetic diversity among elite germplasm resources, leading to a detrimental effect on future wheat production. It is, therefore, necessary to explore new genetic resources for SNS to increase wheat yield. A tetraploid landrace “Ailanmai” × wild emmer wheat recombinant inbred line (RIL) population was used to construct a genetic map using a wheat 55K single- nucleotide polymorphism (SNP) array. The linkage map containing 1,150 bin markers with a total genetic distance of 2,411.8 cm was obtained. Based on the phenotypic data from the eight environments and best linear unbiased prediction (BLUP) values, five quantitative trait loci (QTLs) for SNS were identified, explaining 6.71–29.40% of the phenotypic variation. Two of them, QSns.sau-AM-2B.2 and QSns.sau-AM-3B.2, were detected as a major and novel QTL. Their effects were further validated in two additional F2 populations using tightly linked kompetitive allele-specific PCR (KASP) markers. Potential candidate genes within the physical intervals of the corresponding QTLs were predicted to participate in inflorescence development and spikelet formation. Genetic associations between SNS and other agronomic traits were also detected and analyzed. This study demonstrates the feasibility of the wheat 55K SNP array developed for common wheat in the genetic mapping of tetraploid population and shows the potential application of wheat-related species in wheat improvement programs.