Quantitative Trait Loci For Plant Height Research Articles

Genetic Analysis in Maize Foundation Parents with Mapping Population and Testcross Population: Ye478 Carried More Favorable Alleles and Using QTL Information Could Improve Foundation Parents.

The development of maize foundation parents is an important part of genetics and breeding research, and applying new genetic information to produce foundation parents has been challenging. In this study, we focused on quantitative trait loci (QTLs) and general combining ability (GCA) of Ye478, a widely used foundation parent in China. We developed three sets of populations for QTL mapping and to analyze the GCA for some agronomic traits. The assessment of 15 traits resulted in the detection of 251 QTLs in six tested environments, with 119 QTLs identified through a joint analysis across all environments. Further, analyses revealed that most favorable alleles for plant type-related traits were from Ye478, and more than half of the favorable alleles for yield-related traits were from R08, another foundation parent used in southwestern China, suggesting that different types of foundation parents carried different favorable alleles. We observed that the GCA for most traits (e.g., plant height and 100-kernel weight) was maintained in the inbred lines descended from the foundation parents. Additionally, the continuous improvement in the GCA of the descendants of the foundation parents was consistent with the main trend in maize breeding programs. We identified three significant genomic regions that were highly conserved in three Ye478 descendants, including the stable QTL for plant height. The GCA for the traits in the F7 generation revealed that the QTLs for the given traits per se were affected by additive effects in the same way in different populations.

Application of a library of near isogenic lines to understand context dependent expression of QTL for grain yield and adaptive traits in bread wheat.

BackgroundPrevious quantitative trait loci (QTLs) studies using the Avalon × Cadenza doubled haploid (DH) population identified eleven QTLs determining plant height, heading date and grain yield. The objectives of this study were: (i) to provide insight into the effects of these QTLs using reciprocal multiple near isogenic lines (NILs) with each pair of alleles compared in both parental backgrounds (Avalon or Cadenza), (ii) quantifying epistasis by looking at the background effects and (iii) predict favourable allelic combinations to develop superior genotypes adapted to a target environment.ResultsTo this aim, a library of 553 BC2 NILs and their recurrent parents were tested over two growing seasons (2012/2013 and 2013/2014). The results obtained in the present study validated the plant height, heading date and grain yield QTLs previously identified. Epistatic interactions were detected for the 6B QTL for plant height and heading date, 3A QTL for heading date and grain yield and 2A QTL for grain yield.ConclusionThe marker assisted backcrossing strategy used provided an efficient method of resolving QTL for key agronomic traits in wheat as Mendelian factors determining possible epistatic interactions. The study shows that these QTLs are amenable to marker assisted selection, fine mapping, future positional cloning, and physiological trait dissection.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0849-6) contains supplementary material, which is available to authorized users.

Influence of the Semi‐dwarf Growth Type on Seed Yield and Agronomic Parameters at Low and High Nitrogen Fertilization in Winter Oilseed Rape

In cereals like wheat (Triticum aestivum L.) or rice (Oryza sativa L.), a short‐straw ideotype is characteristic for all modern cultivars, mainly due to the use of genes affecting the dwarf genotype. In oilseed rape (Brassica napus L.), several dwarf mutants are known but so far not widely used. An interesting approach is the production of semi‐dwarf hybrids from dwarf and normal‐type parents, which might have an increased harvest index (HI) and a higher grain yield, especially when nitrogen (N) availability is restricted. To this point, no systematic comparison using a large number of semi‐dwarf and normal‐type hybrids has been published. A double haploid (DH) population was developed that was segregating for the bzh dwarf locus with 54 dwarf and 54 normal‐type lines. By crossing with a normal‐type tester, 108 testcrosses were produced with 54 hybrids each of semi‐dwarf and normal types. These were evaluated under high and zero N fertilization in five and seven environments, respectively, for yield and agronomic parameters. Quantitative trait loci (QTL) were estimated for yield‐relevant traits. Semi‐dwarf hybrids had a significantly higher yield compared with normal types in N‐deficient conditions (2.24 and 2.05 Mg ha−1). At an optimal N supply, no significant difference between growth types was found for seed yield. Oil content was slightly lower in semi‐dwarfs under both N treatments, whereas this was compensated by oil yield. All major QTL for plant height, straw yield, HI, and seed yield co‐segregated with the bzh dwarf locus on linkage group A06, indicating that the dwarf gene is not only reducing plant height but also causing increased HI and higher yield under N limitation for semi‐dwarf hybrids. We conclude that semi‐dwarf hybrids are of high interest for the N‐balanced oilseed rape production, especially when N is scarce.

Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize.

Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.

Identification of Quantitative Trait Loci for Fruit Weight, Soluble Solids Content, and Plant Morphology Using an Introgression Line Population of Solanum pennellii in a Fresh Market Tomato Inbred Line

Introgression lines are convenient populations for the identification, fine-mapping, and functional analysis of genes that are responsible for variations in traits, particularly quantitative trait genes. An introgression line population of Solanum pennellii LA0716 in a fresh market tomato inbred line 1052 was developed by our group. This population was composed of 214 lines. In the present study, five quantitative trait loci (QTLs) for fruit weight, two QTLs for soluble solids content (SSC), three QTLs for plant height, and one QTL for leaf size were identified using this introgression line population. Among these, fw3a and fw4a for fruit weight, ssc7a for SSC, h4t2a, h4t3a, and h4t7a for plant height, and lz12a for leaf size were determined to be novel loci. These results serve as a foundation for fine-mapping and functional analysis of genes underlying these QTLs.

Identification and validation of QTLs controlling multiple traits in sorghum

Sweet sorghum (Sorghum bicolor L. Moench) is a promising crop for biofuel and forage production, having strong resilience to multiple stresses and being capable of thriving on marginal land. The main goals in sweet sorghum improvement are to increase biomass and sugar yield. We validated quantitative trait loci (QTLs) controlling plant height, biomass, juice weight and Brix with 181 recombinant inbred lines derived from a cross between Shihong137, a dwarf grain sorghum, and L-Tian, a tall sweet sorghum, under four environments. Seven QTLs for plant height, stem and leaf fresh weight, stem fresh weight and juice weight could be repeatedly identified across four environments. However, three of those major QTLs, qPH7-2, qSLFW9 and qSFW9, had strong epistatic effect. Many QTLs related to biomass production were co-localised with previously known height QTLs, suggesting that plant height is a major trait regulating biomass production. However, qSFW1-2, qSLFW6-1, and qSLFW6-2 were mapped to positions with no known height QTL. We also identified and validated stable qBrix2 across environments. This study provided a genetic basis for integrated approaches, including plant height, to improve sweet sorghum biomass and sugar production.

A genetic linkage map of coffee (Coffea arabica L.) and QTL for yield, plant height, and bean size

To breed a new variety of coffee (Coffea arabica) requires approximately 25 years due to the long generation time (5–6 years) of this perennial plant and the fact that it takes at least five generations of selection to obtain superior individuals. One way to reduce the number of generations is to use marker-assisted selection (MAS). To implement MAS, it is necessary to develop a genetic map and to identify markers associated with quantitative trait loci (QTLs) governing traits of interest. The objective of this study was to identify QTLs associated with yield, plant height, and bean size. An F2 mapping population consisting of 278 individuals was developed from a cross between Caturra × CCC1046. A total of 338 SSR were used to construct a framework linkage map. Subsequently, SNP markers were added to construct a more robust genetic map. R/qtl software was used to integrate SSR and SNP markers. The integrated linkage map consists of 22 linkage groups populated by 848 SSR and SNP markers, with a total map length of 3800 cM. F3 progenies of the mapping population were planted in five locations and evaluated for yield, plant height, and bean size. A major yield QTL was significant at two locations and a second was significant at one location. Two QTL were each detected for plant height and bean size.

Association Mapping in Scandinavian Winter Wheat for Yield, Plant Height, and Traits Important for Second-Generation Bioethanol Production.

A collection of 100 wheat varieties representing more than 100 years of wheat-breeding history in Scandinavia was established in order to identify marker-trait associations for plant height (PH), grain yield (GY), and biomass potential for bioethanol production. The field-grown material showed variations in PH from 54 to 122 cm and in GY from 2 to 6.61 t ha-1. The release of monomeric sugars was determined by high-throughput enzymatic treatment of ligno-cellulosic material and varied between 0.169 and 0.312 g/g dm for glucose (GLU) and 0.146 and 0.283 g/g dm for xylose (XYL). As expected, PH and GY showed to be highly influenced by genetic factors with repeatability (R) equal to 0.75 and 0.53, respectively, while this was reduced for GLU and XYL (R = 0.09 for both). The study of trait correlations showed how old, low-yielding, tall varieties released higher amounts of monomeric sugars after straw enzymatic hydrolysis, showing reduced recalcitrance to bioconversion compared to modern varieties. Ninety-three lines from the collection were genotyped with the DArTseq® genotypic platform and 5525 markers were used for genome-wide association mapping. Six quantitative trait loci (QTLs) for GY, PH, and GLU released from straw were mapped. One QTL for PH was previously reported, while the remaining QTLs constituted new genomic regions linked to trait variation. This paper is one of the first studies in wheat to identify QTLs that are important for bioethanol production based on a genome-wide association approach.

Inheritance and Identification of a Major Quantitative Trait Locus (QTL) that Confers Resistance to Meloidogyne incognita and a Novel QTL for Plant Height in Sweet Sorghum

Southern root-knot nematodes (Meloidogyne incognita) are a pest on many economically important row crop and vegetable species and management relies on chemicals, plant resistance, and cultural practices such as crop rotation. Little is known about the inheritance of resistance to M. incognita or the genomic regions associated with resistance in sorghum (Sorghum bicolor). In this study, an F2 population (n = 130) was developed between the resistant sweet sorghum cultivar 'Honey Drip' and the susceptible sweet cultivar 'Collier'. Each F2 plant was phenotyped for stalk weight, height, juice Brix, root weight, total eggs, and eggs per gram of root. Strong correlations were observed between eggs per gram of root and total eggs, height and stalk weight, and between two measurements of Brix. Genotyping-by-sequencing was used to generate single nucleotide polymorphism markers. The G-Model, single marker analysis, interval mapping, and composite interval mapping were used to identify a major quantitative trait locus (QTL) on chromosome 3 for total eggs and eggs per gram of root. Furthermore, a new QTL for plant height was also discovered on chromosome 3. Simple sequence repeat markers were developed in the total eggs and eggs per gram of root QTL region and the markers flanking the resistance gene are 4.7 and 2.4 cM away. These markers can be utilized to move the southern root-knot nematode resistance gene from Honey Drip to any sorghum line.

Genetic mapping of common bunt resistance and plant height QTL in wheat.

Breeding for field resistance to common bunt in wheat will need to account for multiple genes and epistatic and QTL by environment interactions. Loci associated with quantitative resistance to common bunt are co-localized with other beneficial traits including plant height and rust resistance. Common bunt, also known as stinking smut, is caused by seed borne fungi Tilletia tritici (Bjerk.) Wint. [syn. Tilletia caries (DC.) Tul.] and Tilletia laevis Kühn [syn. Tilletia foetida (Wallr.) Liro.]. Common bunt is known to cause grain yield and quality losses in wheat due to bunt ball formation and infestation of the grain. The objectives of this research were to identify and map quantitative trait loci (QTL) for common bunt resistance, to study the epistatic interactions between the identified QTL, and investigate the co-localization of bunt resistance with plant height. A population of 261 doubled haploid lines from the cross Carberry/AC Cadillac and checks were genotyped with polymorphic genome wide microsatellite and DArT(®) markers. The lines were grown in 2011, 2012, and 2013 in separate nurseries for common bunt incidence and height evaluation. AC Cadillac contributed a QTL (QCbt.spa-6D) for common bunt resistance on chromosome 6D at markers XwPt-1695, XwPt-672044, and XwPt-5114. Carberry contributed QTL for bunt resistance on chromosomes 1B (QCbt.spa-1B at XwPt743523) 4B (QCbt.spa-4B at XwPt-744434-Xwmc617), 4D (QCbt.spa-4D at XwPt-9747), 5B (QCbt.spa-5B at XtPt-3719) and 7D (QCbt.spa-7D at Xwmc273). Significant epistatic interactions were identified for percent bunt incidence between QCbt.spa-1B × QCbt.spa-4B and QCbt.spa-1B × QCbt.spa-6D, and QTL by environment interaction between QCbt.spa-1B × QCbt.spa-6D. Plant height QTL were found on chromosomes 4B (QPh.spa-4B) and 6D (QPh.spa-6D) that co-located with bunt resistance QTL. The identification of previously unreported common bunt resistance QTL (on chromosomes 4B, 4D and 7D), and new understanding of QTL × QTL interactions will facilitate marker-assisted breeding for common bunt resistance.

Seedling root QTLs analysis on dynamic development and upon nitrogen deficiency stress in Upland cotton

Roots are vital to plant anchorage and efficient uptake of water and nutrients, and play an important role in environmental fitness, performance and yield formation in crops. The main objective of this study was to dissect the developmental behavior of seedling root traits at different developmental stages, and try to explore stress effect of nitrogen deficiency at seedling stage by mapping quantitative trait loci (QTLs) using an intraspecific population of recombinant inbred lines in Upland cotton (Gossypium hirsutum L.). Totally, 34 QTLs and 27 conditional QTLs for root length, root surface area, root volume, number of root tips and number of root forks were detected, respectively, in which 18 were congruent QTLs. The performance of five seedling root traits and QTLs showed obvious dynamic characteristics at three developmental stages. Special conditional QTLs were detected by QTL mapping strategy, in which conditional QTLs with different effects were identified at certain stages, demonstrating that the expression of genes showed temporal characteristics during root development. After nitrogen deprivation and deficiency stress for five days, a total of 11 QTLs were identified. Of these, ten QTLs were also identified in previous three stages under normal nutritional condition, and one QTL qNRT-chr19-1 referring number of root tips was newly detected, which suggested that it might be related to stress response of N-deficiency. After nitrogen deprivation for eight days, a total of 5 QTLs for plant height, maximum root length, fresh weight of root, and root/shoot ratio were identified. These QTLs and dynamic QTLs might offer different clues to understand the developmental mechanism and genetic basis of seedling root traits and to select root trait architecture in breeding program of Upland cotton.

Identification of QTL markers contributing to plant growth, oil yield and fatty acid composition in the oilseed crop Jatropha curcas L.

BackgroundEconomical cultivation of the oilseed crop Jatropha curcas is currently hampered in part due to the non-availability of purpose-bred cultivars. Although genetic maps and genome sequence data exist for this crop, marker-assisted breeding has not yet been implemented due to a lack of available marker–trait association studies. To identify the location of beneficial alleles for use in plant breeding, we performed quantitative trait loci (QTL) analysis for a number of agronomic traits in two biparental mapping populations.ResultsThe mapping populations segregated for a range of traits contributing to oil yield, including plant height, stem diameter, number of branches, total seeds per plant, 100-seed weight, seed oil content and fatty acid composition. QTL were detected for each of these traits and often over multiple years, with some variation in the phenotypic variance explained between different years. In one of the mapping populations where we recorded vegetative traits, we also observed co-localization of QTL for stem diameter and plant height, which were both overdominant, suggesting a possible locus conferring a pleotropic heterosis effect. By using a candidate gene approach and integrating physical mapping data from a recent high-quality release of the Jatropha genome, we were also able to position a large number of genes involved in the biosynthesis of storage lipids onto the genetic map. By comparing the position of these genes with QTL, we were able to detect a number of genes potentially underlying seed traits, including phosphatidate phosphatase genes.ConclusionsThe QTL we have identified will serve as a useful starting point in the creation of new varieties of J. curcas with improved agronomic performance for seed and oil productivity. Our ability to physically map a significant proportion of the Jatropha genome sequence onto our genetic map could also prove useful in identifying the genes underlying particular traits, allowing more controlled and precise introgression of desirable alleles and permitting the pyramiding or stacking of multiple QTL.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-015-0326-8) contains supplementary material, which is available to authorized users.

Two quantitative trait loci for grain yield and plant height on chromosome 3 are tightly linked in coupling phase in rice

Plant height is a very important trait affecting rice production. The introduction of the Green Revolution gene, sd-1, into rice cultivars to create semi-dwarfism has increased grain production. In the development of modern rice breeding, there is an urgent need for a somewhat higher plant for not only maintenance of strong lodging resistance, but also more biomass. In this study, the plant height quantitative trait locus (QTL) qPH3 with moderate effect and the yield per plant QTL qYD3 were identified on chromosome 3 in a population derived from two semi-dwarf cultivars. The 02428 alleles of both QTLs contributed to increasing phenotypic values. In the near-isogenic background, both QTLs exhibited the characteristics of a single Mendelian gene. qPH3 and qYD3 were tightly linked, no more than 130 kb apart, with additive effects of 5.2 cm and 4.4 g, respectively. They were further fine-mapped to a 19-kb region and a 65-kb region, respectively, where the recombination hotspot occurred. The gene encoding gibberellin 20-oxidase associated with plant height was regarded as the candidate of qPH3. Both linked QTLs are in coupling phase, which is convenient for simultaneously selecting both genes for breeding high-yield varieties maintaining strong lodging resistance. Isolation of qYD3 is very promising due to its location in a recombination hotspot region.

A Chromosome Segment Substitution Library of Weedy Rice for Genetic Dissection of Complex Agronomic and Domestication Traits.

Chromosome segment substitution lines (CSSLs) are a powerful alternative for locating quantitative trait loci (QTL), analyzing gene interactions, and providing starting materials for map-based cloning projects. We report the development and characterization of a CSSL library of a U.S. weedy rice accession ‘PSRR-1’ with genome-wide coverage in an adapted rice cultivar ‘Bengal’ background. The majority of the CSSLs carried a single defined weedy rice segment with an average introgression segment of 2.8 % of the donor genome. QTL mapping results for several agronomic and domestication traits from the CSSL population were compared with those obtained from two recombinant inbred line (RIL) populations involving the same weedy rice accession. There was congruence of major effect QTLs between both types of populations, but new and additional QTLs were detected in the CSSL population. Although, three major effect QTLs for plant height were detected on chromosomes 1, 4, and 8 in the CSSL population, the latter two escaped detection in both RIL populations. Since this was observed for many traits, epistasis may play a major role for the phenotypic variation observed in weedy rice. High levels of shattering and seed dormancy in weedy rice might result from an accumulation of many small effect QTLs. Several CSSLs with desirable agronomic traits (e.g. longer panicles, longer grains, and higher seed weight) identified in this study could be useful for rice breeding. Since weedy rice is a reservoir of genes for many weedy and agronomic attributes, the CSSL library will serve as a valuable resource to discover latent genetic diversity for improving crop productivity and understanding the plant domestication process through cloning and characterization of the underlying genes.

Mapping resistant QTLs for rice sheath blight disease with a doubled haploid population

Sheath blight (SB) disease, caused by Rhizoctonia solani Kühn, is one of the most serious diseases causing rice (Oryza sativa L.) yield loss worldwide. A doubled haploid (DH) population was constructed from a cross between a japonica variety CJ06 and an indica variety TN1, and to analyze the quantitative trait loci (QTLs) for SB resistance under three different environments (environments 1–3). Two traits were recorded to evaluate the SB resistance, namely lesion height (LH) and disease rating (DR). Based on field evaluation of SB resistance and a genetic map constructed with 214 markers, a total of eight QTLs were identified for LH and eight QTLs for DR under three environments, respectively. The QTLs for LH were anchored on chromosomes 1, 3, 4, 5, 6, and 8, and explained 4.35–17.53% of the phenotypic variation. The SB resistance allele of qHNLH4 from TN1 decreased LH by 3.08 cm, and contributed to 17.53% of the variation at environment 1. The QTL for LH (qHZaLH8) detected on chromosome 8 in environment 2 explained 16.71% of the variation, and the resistance allele from CJ06 reduced LH by 4.4 cm. Eight QTLs for DR were identified on chromosomes 1, 5, 6, 8, 9, 11, and 12 under three conditions with the explained variation from 2.0 to 11.27%. The QTL for DR (qHZaDR8), which explained variation of 11.27%, was located in the same interval as that of qHZaLH8, both QTLs were detected in environment 2. A total of six pairs of digenic epistatic loci for DR were detected in three conditions, but no epistatic locus was observed for LH. In addition, we detected 12 QTLs for plant height (PH) in three environments. None of the PH-QTLs were co-located with the SB-QTLs. The results facilitate our understanding of the genetic basis for SB resistance in rice.

Genetic architecture of fusarium head blight resistance in four winter triticale populations.

Fusarium head blight (FHB) is a devastating disease that causes significant reductions in yield and quality in wheat, rye, and triticale. In triticale, knowledge of the genetic architecture of FHB resistance is missing but essential due to modern breeding requirements. In our study, four doubled-haploid triticale populations (N=120 to 200) were evaluated for resistance to FHB caused by artificial inoculation with Fusarium culmorum in four environments. DArT markers were used to genotype triticale populations. Seventeen quantitative trait loci (QTL) for FHB resistance were detected across all populations; six of them were derived from rye genome and located on chromosomes 4R, 5R, and 7R, which are here reported for the first time. The total cross-validated ratio of the explained phenotypic variance for all detected QTL in each population was 41 to 68%. In all, 17 QTL for plant height and 18 QTL for heading stage were also detected across all populations; 3 and 5 of them, respectively, were overlapping with QTL for FHB. In conclusion, FHB resistance in triticale is caused by a multitude of QTL, and pyramiding them contributes to higher resistance.

Using the UK reference population Avalon×Cadenza as a platform to compare breeding strategies in elite Western European bread wheat.

Wheat breeders select for qualitative and quantitative traits, the latter often detected as quantitative trait loci (QTL). It is, however, a long procedure from QTL discovery to the successful introduction of favourable alleles into new elite varieties and finally into farmers’ crops. As a proof of principle for this process, QTL for grain yield (GY), yield components, plant height (PH), ear emergence (EM), solid stem (SS) and yellow rust resistance (Yr) were identified in segregating UK bread wheat reference population, Avalon × Cadenza. Among the 163 detected QTL were several not reported before: 17 for GY, the major GY QTL on 2D; a major SS QTL on 3B; and Yr6 on 7B. Common QTL were identified on ten chromosomes, most interestingly, grain number (GN) was found to be associated with Rht-D1b; and GY and GN with a potential new allele of Rht8. The interaction of other QTL with GY and yield components was discussed in the context of designing a UK breeding target genotype. Desirable characteristics would be: similar PH and EM to Avalon; Rht-D1b and Vrn-A1b alleles; high TGW and GN; long and wide grains; a large root system, resistance to diseases; and maximum GY. The potential of the identified QTL maximising transgressive segregation to produce a high-yielding and resilient genotype was demonstrated by simulation. Moreover, simulating breeding strategies with F2 enrichment revealed that the F2–DH procedure was superior to the RIL and the modified SSD procedure to achieve that genotype. The proposed strategies of parent selection and breeding methodology can be used as guidance for marker-assisted wheat breeding.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-015-0268-7) contains supplementary material, which is available to authorized users.

A linkage map of chickpea (Cicer arietinum L.) based on population from ILC3279×ILC588 crosses: Location of genes for time to flowering, seed size and plant height

Quantitative traits of seed size, plant height and days to flowering were studied in a chickpea intraspecific F3:4 lines population derived from a ILC3279?ILC588 cross. The lines were genotyped with random amplified polymorphic DNA (RAPD), universal rice primer (URP) and sequence tagged microsatellite site (STMS) markers, and a genetic map composed of 7 linkage groups (LGs) covering 285.3 cM was constructed. Quantitative trait loci (QTLs) for the three characters were detected in LG2, LG3 and LG4. Two QTLs for days to flowering were detected on LG2 and LG3. These two QTLs accounted for 58% of the total phenotypic variation for days to flowering. A QTL for plant height was located in LG3 explaining around 42% of the variation. This trait was shown to be under a major gene control. For 100-seed weight, a QTL located in LG4 explained around 37% of the phenotypic variations. This information can be used to formulate the an efficient breeding strategy for improvement of time to flowering in short-season temperate environments, plant height with more reproductive biomass and improved yield with bigger seed size in chickpea.

QTL mapping for plant height and yield components in common wheat under water-limited and full irrigation environments

Plant height (PH) and yield components are important traits for yield improvement in wheat breeding. In this study, 207 F2:4 recombinant inbred lines (RILs) derived from the cross Jingdong 8/Aikang 58 were investigated under limited and full irrigation environments at Beijing and Gaoyi, Hebei province, during the 2011–12 and 2012–13 cropping seasons. The RILs were genotyped with 149 polymorphic simple sequence repeat (SSR) markers, and quantitative trait loci (QTLs) for PH and yield components were analysed by inclusive composite interval mapping. All traits in the experiment showed significant genetic variation and interaction with environments. The range of broad-sense heritabilities of PH, 1000-kernel weight (TKW), number of kernels per spike (KNS), number of spikes per m2 (NS), and grain yield (GY) were 0.97–0.97, 0.87–0.89, 0.59–0.61, 0.58–0.68, and 0.23–0.48. The numbers of QTLs detected for PH, TKW, KNS, NS, and GY were 3, 10, 8, 7 and 9, respectively, across all eight environments. PH QTLs on chromosomes 4D and 6A, explaining 61.3–80.2% of the phenotypic variation, were stably expressed in all environments. QPH.caas-4D is assumed to be the Rht-D1b locus, whereas QPH.caas-6A is likely to be a newly discovered gene. The allele from Aikang 58 at QPH.caas-4D reduced PH by 11.5–18.2% and TKW by 2.6–3.8%; however, KNS increased (1.2–3.7%) as did NS (2.8–4.1%). The QPH.caas-6A allele from Aikang 58 reduced PH by 8.0–11.5% and TKW by 6.9–8.5%, whereas KNS increased by 1.2–3.6% and NS by 0.9–4.5%. Genotypes carrying both QPH.caas-4D and QPH.caas-6A alleles from Aikang 58 showed reduced PH by 28.6–30.6%, simultaneously reducing TKW (13.8–15.2%) and increasing KNS (3.4–4.9%) and NS (6.5–10%). QTKW.caas-4B and QTKW.caas-5B.1 were stably detected and significantly associated with either KNS or NS. Major KNS QTLs QKNS.caas-4B and QKNS.caas-5B.1 and the GY QTL QGY.caas-3B.2 were detected only in water-limited environments. The major TKW QTKW.caas-6D had no significant effect on either KNS or NS and it could have potential for improving yield.

SNP markers linked to QTL conditioning plant height, lodging, and maturity in soybean

Soybean (Glycine max L. Merr.) is a major crop and a leading source of protein meal and edible oil worldwide. Plant height (PHT), lodging (LDG), and days to maturity (MAT) are three important agronomic traits that influence the seed yield of soybean. The objective of this study was to map quantitative trait loci (QTL) for PHT, LDG and MAT using a high density SNP map of a recombinant inbred line soybean mapping population. With single factor analysis of variance six, four, and three QTL were identified across environments for PHT, LDG, and MAT, respectively. Several QTL for each trait were also detected by composite interval mapping with high confidence. Two and one QTL for PHT and LDG, respectively were novel QTL identified in this study. Additionally, most QTL identified in the present study are flanked by two or more SNP markers that are closely linked to each QTL. The SNP markers identified to be closely linked to each QTL in this study are valuable for marker assisted selection (MAS) of the QTL by interested soybean breeding programs. Thus, this study clearly advances the knowledge on genetic controls of plant height, lodging and maturity in soybean, and identifies more efficient and reliable markers for MAS for these traits than those currently exist.