Minor-effect Quantitative Trait Loci Research Articles

Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon.

The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.

Quantitative Trait Locus Mapping by Whole Genome Re-Sequencing and Analysis of Candidate Genes for Heading Date in Rice

Heading date (HD) is a critical traits of rice that significantly affects yield and quality. Although researchers identified major-effect genes that involving in HD, they often have dramatic effects on HD and other vital agronomic traits, making them not easy to be applied in molecular breeding practices. To address this constraint, we focused on identifying genes with minor effects on HD that allow fine-tuning flowering time without significant yield loss. Previously, a 150-recombinant inbred lines (RILs) population was constructed from the early-heading date variety V20B and the lateheading variety CPSLO17, and the line RIL-111 showed the intermediate phenotype of heading date between V20B and CPSLO17. In our work, we applied bulked segregant analysis (BSA) with whole genome re-sequencing (WGS) to map quantitative trait locus (QTL) for heading date. In the results, a minor effect QTL, designated as qDTHR, was identified within the 647.1 kb on chromosome 1 of the F2 population, constructed from RIL-111 and V20B, associating with 14 non-synonymous mutant genes in the interval. The results provide a basis for molecular breeding to improve rice varieties, and lay a foundation for further cloning and functional analysis.

QTG-Miner aids rapid dissection of the genetic base of tassel branch number in maize

Genetic dissection of agronomic traits is important for crop improvement and global food security. Phenotypic variation of tassel branch number (TBN), a major breeding target, is controlled by many quantitative trait loci (QTLs). The lack of large-scale QTL cloning methodology constrains the systematic dissection of TBN, which hinders modern maize breeding. Here, we devise QTG-Miner, a multi-omics data-based technique for large-scale and rapid cloning of quantitative trait genes (QTGs) in maize. Using QTG-Miner, we clone and verify seven genes underlying seven TBN QTLs. Compared to conventional methods, QTG-Miner performs well for both major- and minor-effect TBN QTLs. Selection analysis indicates that a substantial number of genes and network modules have been subjected to selection during maize improvement. Selection signatures are significantly enriched in multiple biological pathways between female heterotic groups and male heterotic groups. In summary, QTG-Miner provides a large-scale approach for rapid cloning of QTGs in crops and dissects the genetic base of TBN for further maize breeding.

Genetic architecture of microhabitat adaptation traits in a pair of sympatric Primulina species

Exploring the genetic basis of adaptive divergence at fine spatial scales can broaden our basic understanding of evolution and how organisms may adapt to changing environments in the future. Cave-associated microhabitats provide a unique opportunity to gain insight into microgeographic adaptation. We studied the genetic architecture of microhabitat-related divergence in flower phenology and leaf traits between two sister species of Primulina, P. depressa and P. danxiaensis, which live in sympatry but occupy contrasting microhabitats. We identified 40 significant quantitative trait loci (QTLs) associated with the interspecific differences in these microhabitat adaptation traits. Flowering time was controlled by one major-effect and six minor-effect QTLs, while leaf traits were influenced by 9–12 QTLs of small to moderate effect. The genetic architecture of the flowering time and the specific leaf area was genetically independent of other traits. Our results suggest that microhabitat adaptation in sympatric populations of Primulina differs according to different traits, with leaf traits diverging with the accumulation of many small changes and flowering phenology being driven by major effect variance.

Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.).

Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32-25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.

Genome wide association study to detect genetic regions related to isoflavone content in a mutant soybean population derived from radiation breeding.

Isoflavones are major secondary metabolites that are exclusively produced by legumes, including soybean. Soy isoflavones play important roles in human health as well as in the plant defense system. The isoflavone content is influenced by minor-effect quantitative trait loci, which interact with polygenetic and environmental factors. It has been difficult to clarify the regulation of isoflavone biosynthesis because of its complex heritability and the influence of external factors. Here, using a genotype-by-sequencing-based genome-wide association mapping study, 189 mutant soybean genotypes (the mutant diversity pool, MDP) were genotyped on the basis of 25,646 high-quality single nucleotide polymorphisms (SNPs) with minor allele frequency of >0.01 except for missing data. All the accessions were phenotyped by determining the contents of 12 isoflavones in the soybean seeds in two consecutive years (2020 and 2021). Then, quantitative trait nucleotides (QTNs) related to isoflavone contents were identified and validated using multi-locus GWAS models. A total of 112 and 46 QTNs related to isoflavone contents were detected by multiple MLM-based models in 2020 and 2021, respectively. Of these, 12 and 5 QTNs were related to more than two types of isoflavones in 2020 and 2021, respectively. Forty-four QTNs were detected within the 441-Kb physical interval surrounding Gm05:38940662. Of them, four QTNs (Gm05:38936166, Gm05:38936167, Gm05:38940662, and Gm05:38940717) were located at Glyma.05g206900 and Glyma.05g207000, which encode glutathione S-transferase THETA 1 (GmGSTT1), as determined from previous quantitative trait loci annotations and the literature. We detected substantial differences in the transcript levels of GmGSTT1 and two other core genes (IFS1 and IFS2) in the isoflavone biosynthetic pathway between the original cultivar and its mutant. The results of this study provide new information about the factors affecting isoflavone contents in soybean seeds and will be useful for breeding soybean lines with high and stable concentrations of isoflavones.

Fine Mapping of qTGW7b, a Minor Effect QTL for Grain Weight in Rice (Oryza sativa L.).

Grain weight is a key trait that determines rice quality and yield, and it is primarily controlled by quantitative trait loci (QTL). Recently, attention has been paid to minor QTLs. A minor effect QTL qTGW7 that controls grain weight was previously identified in a set of chromosomal fragment substitution lines (CSSLs) derived from Nipponbare (NPB)/93-11. Compared to NPB, the single segment substitution line (SSSL) N83 carrying the qTGW7 introgression exhibited an increase in grain length and width and a 4.5% increase in grain weight. Meanwhile, N83 was backcrossed to NPB to create a separating population, qTGW7b, a QTL distinct from qTGW7, which was detected between markers G31 and G32. Twelve near-isogenic lines (NILs) from the BC9F3 population and progeny of five NILs from the BC9F3:4 population were genotyped and phenotyped, resulting in the fine mapping of the minor effect QTL qTGW7b to the approximately 86.2-kb region between markers G72 and G32. Further sequence comparisons and expression analysis confirmed that five genes, including Os07g39370, Os07g39430, Os07g39440, Os07g39450, and Os07g39480, were considered as the candidate genes underlying qTGW7b. These results provide a crucial foundation for further cloning of qTGW7b and molecular breeding design in rice.

Pseudomonas phaseolicola preferentially modulates genes encoding leucine-rich repeat and malectin domains in the bean landrace G2333

Main conclusionCandidate resistance genes encoding malectin-like and LRR domains mapped to halo blight resistance loci throughout the common bean genome are co-expressed to fight a range of Pph races.Common bean (Phaseolus vulgaris L.) is an important crop both as a source of protein and other nutrients for human nutrition and as a nitrogen fixer that benefits sustainable agriculture. This crop is affected by halo blight disease, caused by the bacterium Pseudomonas syringae pv. phaseolicola (Pph), which can lead to 45% yield losses. Common bean resistance to Pph is conferred by six loci (Pse-1 to Pse-6) and minor-effect quantitative trait loci (QTLs); however, information is lacking on the molecular mechanisms implicated in this resistance. Here, we describe an in-depth RNA-sequencing (RNA-seq) analysis of the tolerant G2333 bean line in response to the Pph strain NPS3121. We identified 275 upregulated and 357 downregulated common bean genes in response to Pph infection. These differentially expressed genes were mapped to all 11 chromosomes of P. vulgaris. The upregulated genes were primarily components of plant immune responses and negative regulation of photosynthesis, with enrichment for leucine-rich repeat (LRRs) and/or malectin-like carbohydrate-binding domains. Interestingly, LRRs and malectin genes mapped to the same location as previously identified Pph resistance loci or QTLs. For instance, the major loci Pse-6/HB4.2 involved in broad-resistance to many Pph races co-located with induced LRR-encoding genes on Pv04. These findings indicate a coordinated modulation of genes involved in pathogen perception and signal transduction. In addition, the results further support these LRR/malectin loci as resistance genes in response to halo blight. Thus, these genes are potential targets for future genetic manipulation, enabling the introduction of resistance to Pph into elite cultivars of common bean.

Mapping novel QTLs for yield related traits from a popular rice hybrid KRH-2 derived doubled haploid (DH) population.

The online version contains supplementary material available at 10.1007/s13205-021-03045-7.

Maize streak virus research in Africa: an end or a crossroad.

The economic importance of the maize streak virus disease to the African maize production dynamic is to be appreciated now more than ever due to the preponderant influence of a changing climate. Continued dependence on a single major-effect quantitative trait locus (QTL) called Msv1 on Chromosome 1 of Maize (Zea mays L.) is not guaranteed to ensure durable resistance to the causal pathogen. With over ten decades of research on the disease and its associated host plant resistance mechanisms, it is pertinent to consider future approaches to attaining durability by looking to the synergistic roles of moderate- and minor-effect QTLs located on other chromosomes so as to facilitate a secure farming system for sub-Saharan Africa. For this review, more than 40 publications relating to maize streak disease research were methodically analysed with about 30% making specific reference to conventional, molecular and transgenic approaches employed in introgressing, maintaining and improving streak resistance in maize. A meta-analysis of mapped QTLs conferring streak resistance was conducted in a bid to reveal any inter-dependence or co-localization of resistant loci and to aid decision-making for marker-assisted breeding. With the changing climatic conditions around the globe, man's preparedness in the event of an epidemic following any evolutionary process in the streak viral genome was determined as insufficient. Modern breeding approaches including gene pyramiding that could be considered in maize breeding programmes to ensure durability for streak resistance were proposed while improving maize for other abiotic stress tolerance, particularly drought.

Mapping and Validation of a Stable Quantitative Trait Locus Conferring Maize Resistance to Gibberella Ear Rot.

Gibberella ear rot (GER), a prevalent disease caused by Fusarium graminearum, can result in significant yield loss and carcinogenic mycotoxin contamination in maize worldwide. However, only a few quantitative trait loci (QTLs) for GER resistance have been reported. In this study, we evaluated a Chinese recombinant inbred line (RIL) population comprising 204 lines, developed from a cross between a resistant parent DH4866 and a susceptible line T877, in three field trials under artificial inoculation with F. graminearum. The RIL population and their parents were genotyped with an Affymetrix microarray CGMB56K SNP Array. Based on the genetic linkage map constructed using 1,868 bins as markers, 11 QTLs, including five stable QTLs, were identified by individual environment analysis. Joint multiple environments analysis and epistatic interaction analysis revealed six additive and six epistatic (additive × additive) QTLs, respectively. None of the QTLs could explain more than 10% of phenotypic variation, suggesting that multiple minor-effect QTLs contributed to the genetic component of resistance to GER, and both additive and epistatic effects contributed to the genetic architecture of resistance to GER. A novel QTL, qGER4.09, with the largest effect, identified and validated using 588 F2 individuals, was colocalized with genomic regions for Fusarium ear rot and Aspergillus ear rot, indicating that this genetic locus likely confers resistance to multiple pathogens and can potentially be utilized in breeding maize varieties aimed at improving the resistance not only to GER but also other ear rot diseases.

Mapping QTL associated with partial resistance to Aphanomyces root rot in pea (Pisum sativum L.) using a 13.2K SNP array and SSR markers.

A stable and major QTL, which mapped to an approximately 20.0cM region on pea chromosome 4, was identified as the most consistent region conferring partial resistance to Aphanomyces euteiches. Aphanomyces root rot (ARR), caused by Aphanomyces euteiches Drechs., is a destructive soilborne disease of field pea (Pisum Sativum L.). No completely resistant pea germplasm is available, and current ARR management strategies rely on partial resistance and fungicidal seed treatments. In this study, an F8 recombinant inbred line population of 135 individuals from the cross 'Reward' (susceptible) × '00-2067' (tolerant) was evaluated for reaction to ARR under greenhouse conditions with the A. euteiches isolate Ae-MDCR1 and over 2years in a field nursery in Morden, Manitoba. Root rot severity, foliar weight, plant vigor and height were used as estimates of tolerance to ARR. Genotyping was conducted with a 13.2K single-nucleotide polymorphism (SNP) array and 222 simple sequence repeat (SSR) markers. Statistical analyses of the phenotypic data indicated significant (P < 0.001) genotypic effects and significant G × E interactions (P < 0.05) in all experiments. After filtering, 3050 (23.1%) of the SNP and 30 (13.5%) of the SSR markers were retained for linkage analysis, which distributed 2999 (2978 SNP + 21 SSR) of the markers onto nine linkage groups representing the seven chromosomes of pea. Mapping of quantitative trait loci (QTL) identified 8 major-effect (R2 > 20%), 13 moderate-effect (10% < R2 < 20%) effect and 6 minor-effect (R2 < 10%) QTL. A genomic region on chromosome 4, delimited by the SNP markers PsCam037549_22628_1642 and PsCam026054_14999_2864, was identified as the most consistent region responsible for partial resistance to A. euteiches isolate Ae-MDCR1. Other genomic regions important for resistance were of the order chromosome 5, 6 and 7.

Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents.

Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.

Genome-Wide Mapping of Loci for Adult-Plant Resistance to Stripe Rust in Durum Wheat Svevo Using the 90K SNP Array.

Stripe rust is a foliar disease in wheat caused by Puccinia striiformis f. tritici. The best way to protect wheat from this disease is by growing resistant cultivars. Tetraploid wheat can serve as a good source of valuable genetic diversity for various traits. Here, we report the mapping of nine stripe rust resistance quantitative trait loci (QTL) effective against P. striiformis f. tritici in China and Israel. We used recombinant inbred lines (RILs) developed from a cross between the durum wheat cultivar Svevo and Triticum dicoccoides accession Zavitan. By genotyping the RIL population of 137 lines using the wheat 90K single-nucleotide polymorphism array, we mapped an adult-plant resistance locus QYrsv.swust-1BL.1, the most effective QTL, within a 0.75-centimorgan region in T. turgidum subsp. durum 'Svevo' on chromosome arm 1BL, corresponding to the region of 670.7 to 671.5 Mb on the Chinese Spring chromosome arm 1BL. Of the other eight minor-effect stripe rust QTL, seven were from Svevo and mapped on chromosomes 1A, 1B, 2B, 3A, 4A, and 5A, and one was from Zavitan and mapped on chromosome 2A. Several QTL with epistatic effects were identified as well. The markers linked to the resistance QTL can be useful in marker-assisted selection for incorporation of these resistance QTL into both durum and common wheat cultivars.

Linkage mapping and QTL analysis of pecan (Carya illinoinensis) full-siblings using genotyping-by-sequencing

Pecan (Carya illinoinensis) is a nut-producing tree native to North America grown for its culinary, ornamental, and lumber characteristics. A newly developed chromosome-scale reference genome for pecan was used to create genotyping-by-sequencing (GBS)-based high-density genetic linkage maps of 151 full-sibling progeny of ‘Elliott’ and ‘VC1-68’. These maps incorporate 6142 SNPs segregating in a testcross pattern into 32 linkage groups representing the 16 chromosomes of pecan across the two parents. The average distance between markers was 0.46 cM and the two maps totaled 1376.4 cM and 1463.1 cM for ‘Elliott’ and ‘VC1-68’, respectively. These markers, plus an additional 1096 intercross markers, were used to create a 1557.8-cM pecan consensus genetic linkage map. Quantitative trait locus (QTL) analyses revealed 1 major and 2 minor effect QTL for budbreak and 1 minor effect QTL for pecan scab susceptibility. The major effect locus inherited from ‘VC1-68’ explained up to 30% of the variation in budbreak and appeared across 3 years of observations. This QTL is syntenic to recently identified major effect QTL for budbreak in English walnut. The techniques reported herein, and the resulting genetic maps will facilitate future discoveries of valuable fruiting trait loci as this pecan population completes the transition to sexual maturity. In addition, the major budbreak QTL coincident in pecan and English walnut may represent a conserved mechanism effecting budbreak across the Juglandaceae providing critical knowledge for future investigations of variability in phenology.

Finding new addictive QTL for yield traits based on a high-density genetic map in hybrid rice

Rice is one of the most important food crops in the world. To discover the genetic basis of yield components in super hybrid rice Nei2You No.6, 386 recombinant inbred sister lines (RISLs) were obtained for mapping quantitative trait loci (QTL) responsible for grain yield per plant, number of panicles per plant, grain number per panicle and 1000-grain weight. Using whole genome re-sequencing, a high-density linkage map consisting of 3203 Bin markers was constructed with total genetic coverage of 1951.1 cM and average density of 0.61 cM. A total of 43 yield-related QTL were mapped to all 12 chromosomes, and each explained 2.40–10.17% phenotypic variance, indicating that the medium and minor effect QTL are genetic basis for high yield of Nei2You No.6. With positive effect, 28 out of the 43 QTL are inherited from the maintainer line (Nei2B). Nine loci, qGYP-6b, qGNP-6c, qNP-7, qTGW-1a, qTGW-5, qTGW-7, qTGW-10b, qTGW-10c and qTGW-12 showed stable effects across multiple environments. Five of these nine QTL were co-located with previously reported QTL, and four novel locus, qNP-7, qGNP-6c, qTGW-7 and qTGW-12, were firstly identified in the present study. Subsequently, qNP-7, qTGW-7 and qTGW-12 were validated using corresponding paired sister lines which differed only in the target genome region. The recombinant inbred sister lines is an effective tool for mapping and confirming QTL of yield-associated traits. Newly detected QTL provide new resource for investigating genetics of yield components and will accelerate molecular breeding in rice.

Genetic dissection of husk number and length across multiple environments and fine-mapping of a major-effect QTL for husk number in maize (Zea mays L.)

Husk number (HN) and husk length (HL) influence the mechanical harvesting of maize grain. We investigated the genetic basis of HN and HL using a population of 204 recombinant inbred lines phenotypically evaluated in five environments. The two husk traits showed broad phenotypic variation and high heritability. Nine stable quantitative trait loci (QTL) were identified by single-environment mapping, comprising four QTL for HN and five for HL, and three QTL explained >10% of the phenotypic variation. Joint mapping revealed 22 additive QTL and 46 epistatic QTL. Both additive and epistatic (additive × additive) effects as well as a few large-effect QTL and some minor-effect QTL appeared to contribute to the genetic architecture of HN and HL. The QTL for HN located on chromosome 7, qHN7, which accounted for ~20% of phenotypic variation, was detected in all five environments. qHN7 was fine-mapped to a 721.1 kb physical region based on the maize B73 RefGen_v3 genome assembly. Within this interval, four genes associated with plant growth and development were selected as candidate genes. The results will be useful for improvement of maize husk traits by molecular breeding and provide a basis for the cloning of qHN7.

Genetic mapping and genomic selection for maize stalk strength

BackgroundMaize is one of the most important staple crops and is widely grown throughout the world. Stalk lodging can cause enormous yield losses in maize production. However, rind penetrometer resistance (RPR), which is recognized as a reliable measurement to evaluate stalk strength, has been shown to be efficient and useful for improving stalk lodging-resistance. Linkage mapping is an acknowledged approach for exploring the genetic architecture of target traits. In addition, genomic selection (GS) using whole genome markers enhances selection efficiency for genetically complex traits. In the present study, two recombinant inbred line (RIL) populations were utilized to dissect the genetic basis of RPR, which was evaluated in seven growth stages.ResultsThe optimal stages to measure stalk strength are the silking phase and stages after silking. A total of 66 and 45 quantitative trait loci (QTL) were identified in each RIL population. Several potential candidate genes were predicted according to the maize gene annotation database and were closely associated with the biosynthesis of cell wall components. Moreover, analysis of gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway further indicated that genes related to cell wall formation were involved in the determination of RPR. In addition, a multivariate model of genomic selection efficiently improved the prediction accuracy relative to a univariate model and a model considering RPR-relevant loci as fixed effects.ConclusionsThe genetic architecture of RPR is highly genetically complex. Multiple minor effect QTL are jointly involved in controlling phenotypic variation in RPR. Several pleiotropic QTL identified in multiple stages may contain reliable genes and can be used to develop functional markers for improving the selection efficiency of stalk strength. The application of genomic selection to RPR may be a promising approach to accelerate breeding process for improving stalk strength and enhancing lodging-resistance.

The genetic basis of hybrid male sterility in sympatric Primulina species

BackgroundSympatric sister species provide an opportunity to investigate the genetic mechanisms and evolutionary forces that maintain species boundaries. The persistence of morphologically and genetically distinct populations in sympatry can only occur if some degree of reproductive isolation exists. A pair of sympatric sister species of Primulina (P. depressa and P. danxiaensis) was used to explore the genetic architecture of hybrid male sterility.ResultsWe mapped one major- and seven minor-effect quantitative trait loci (QTLs) that underlie pollen fertility rate (PFR). These loci jointly explained 55.4% of the phenotypic variation in the F2 population. A Bateson–Dobzhansky–Muller (BDM) model involving three loci was observed in this system. We found genotypic correlations between hybrid male sterility and flower morphology, consistent with the weak but significant phenotypic correlations between PFR and floral traits.ConclusionsHybrid male sterility in Primulina is controlled by a polygenic genetic basis with a complex pattern. The genetic incompatibility involves a three-locus BDM model. Hybrid male sterility is genetically correlated with floral morphology and divergence hitchhiking may occur between them.

Multi-environment QTL mapping of crown root traits in a maize RIL population

Crown root traits, including crown root angle (CRA), diameter (CRD), and number (CRN), are major determining factors of root system architecture, which influences crop production. In maize, the genetic mechanisms determining crown root traits in the field are largely unknown. CRA, CRD, and CRN were evaluated in a recombinant inbred line population in three field trials. High phenotypic variation was observed for crown root traits, and all measured traits showed significant genotype–environment interactions. Single-environment (SEA) and multi-environment (MEA) quantitative trait locus (QTL) analyses were conducted for CRA, CRD, and CRN. Of 46 QTL detected by SEA, most explained less than 10% of the phenotypic variation, indicating that a large number of minor-effect QTL contributed to the genetic component of these traits. MEA detected 25 QTL associated with CRA, CRD, and CRN, and 2 and 1 QTL were identified with significant QTL-by-environment interaction effects for CRA and CRD, respectively. A total of 26.1% (12/46) of the QTL identified by SEA were also detected by MEA, with many being detected in more than one environment. These findings contribute to our understanding of the phenotypic and genotypic patterns of crown root traits in different environments. The identified environment-specific QTL and stable QTL may be used to improve root traits in maize breeding.