Analyses of quantitative trait loci associated with resistance to shape Sclerotinia sclerotiorum in sunflowers (shape Helianthus annuus L.) using molecular markers

Restriction fragment length polymorphism and isoenzyme markers were used to investigate quantitative trait loci involved in sunflower resistance to mycelial extension of Sclerotinia sclerotiorum on leaves and capitula. Seed weight, oil content and flowering data were also evaluated. Four quantitative trait loci were demonstrated for leaf resistance and two for capitulum resistance. One of these zones appears involved in resistance to both types of S. sclerotiorum attack while the others appear specific for resistance of one part of the plant. Two quantitative trait loci were detected for seed weight, three for oil content and three for flowering date. Individual quantitative trait loci explained 9% to 48% of the phenotypic variability, confirming the polygenic basis of the quantitative traits studied. Overall, the quantitative trait loci explain 60% of the genetic variation for leaf resistance and 38% for capitulum resistance to S. sclerotiorum. One linkage group is particularly interesting since it includes quantitative trait loci for all the five quantitative traits measured. Hypotheses for linkage versus pleiotropy and consequences of all the results in resistance breeding are discussed.     

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS

Landraces often contain genetic diversity that has been lost in modern cultivars, including alleles that confer enhanced local adaptation. To comprehensively identify loci associated with adaptive traits in soya bean landraces, for example flowering time, a population of 1938 diverse landraces and 97 accessions of the wild progenitor of cultivated soya bean, Glycine soja was genotyped using tGBS^®. Based on 99 085 high‐quality SNPs, landraces were classified into three sub‐populations which exhibit geographical genetic differentiation. Clustering was inferred from STRUCTURE, principal component analyses and neighbour‐joining tree analyses. Using phenotypic data collected at two locations separated by 10 degrees of latitude, 17 trait‐associated SNPs (TASs) for flowering time were identified, including a stable locus Chr12:5914898 and previously undetected candidate QTL/genes for flowering time in the vicinity of the previously cloned flowering genes, E1 and E2. Using passport data associated with the collection sites of the landraces, 27 SNPs associated with adaptation to three bioclimatic variables (temperature, daylength, and precipitation) were identified. A series of candidate flowering genes were detected within linkage disequilibrium (LD) blocks surrounding 12 bioclimatic TASs. Nine of these TASs exhibit significant differences in flowering time between alleles within one or more of the three individual sub‐populations. Signals of selection during domestication and/or subsequent landrace diversification and adaptation were detected at 38 of the 44 flowering and bioclimatic TASs. Hence, this study lays the groundwork to begin breeding for novel environments predicted to arise following global climate change.     

Genome‐wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China

Bread wheat is a leading cereal crop worldwide. Limited amount of superior allele loci restricted the progress of molecular improvement in wheat breeding. Here, we revealed new allelic variation distribution for 13 yield‐related traits in series of genome‐wide association studies (GWAS) using the wheat 90K genotyping assay, characterized in 163 bread wheat cultivars. Agronomic traits were investigated in 14 environments at three locations over 3 years. After filtering SNP data sets, GWAS using 20 689 high‐quality SNPs associated 1769 significant loci that explained, on average, ~20% of the phenotypic variation, both detected already reported loci and new promising genomic regions. Of these, repetitive and pleiotropic SNPs on chromosomes 6AS, 6AL, 6BS, 5BL and 7AS were significantly linked to thousand kernel weight, for example BS00021705_51 on 6BS and wsnp_Ex_c32624_41252144 on 6AS, with phenotypic variation explained (PVE) of ~24%, consistently identified in 12 and 13 of the 14 environments, respectively. Kernel length‐related SNPs were mainly identified on chromosomes 7BS, 6AS, 5AL and 5BL. Plant height‐related SNPs on chromosomes 4DS, 6DL, 2DS and 1BL were, respectively, identified in more than 11 environments, with averaged PVE of ~55%. Four SNPs were confirmed to be important genetic loci in two RIL populations. Based on repetivity and PVE, a total of 41 SNP loci possibly played the key role in modulating yield‐related traits of the cultivars surveyed. Distribution of superior alleles at the 41 SNP loci indicated that superior alleles were getting popular with time and modern cultivars had integrated many superior alleles, especially for peduncle length‐ and plant height‐related superior alleles. However, there were still 19 SNP loci showing less than percentages of 50% in modern cultivars, suggesting they should be paid more attention to improve yield‐related traits of cultivars in the Yellow and Huai wheat region. This study could provide useful information for dissection of yield‐related traits and valuable genetic loci for marker‐assisted selection in Chinese wheat breeding programme.     

Identifying SNP markers tightly associated with six major genes in peach [<Emphasis Type="Italic">Prunus persica</Emphasis> (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)

One of the applications of genomics is to identify genetic markers linked to loci responsible for variation in phenotypic traits, which could be used in breeding programs to select individuals with favorable alleles, particularly at the seedling stage. With this aim, in the framework of the European project FruitBreedomics, we selected five main peach fruit characters and a resistance trait, controlled by major genes with Mendelian inheritance: fruit flesh color Y, fruit skin pubescence G, fruit shape S, sub-acid fruit D, stone adhesion-flesh texture F-M, and resistance to green peach aphid Rm2. They were all previously mapped in Prunus. We then selected three F₁ and three F₂ progenies segregating for these characters and developed genetic maps of the linkage groups including the major genes, using the single nucleotide polymorphism (SNP) genome-wide scans obtained with the International Peach SNP Consortium (IPSC) 9K SNP array v1. We identified SNPs co-segregating with the characters in all cases. Their positions were in agreement with the known positions of the major genes. The number of SNPs linked to each of these, as well as the size of the physical regions encompassing them, varied depending on the maps. As a result, the number of useful SNPs for marker-assisted selection varied accordingly. As a whole, this study establishes a sound basis for further development of MAS on these characters. Additionally, we also discussed some limitations that were observed regarding the SNP array efficiency.     

灯盏花种质资源群体表型多样性研究

以采集自云南和贵州的21份灯盏花种质资源为材料,观测了它们的群体表型性状特征,并分析了这些表型性状的遗传多样性.结果表明:灯盏花种质资源的表型质量性状在居群内外均有丰富变异,不同质量性状的频率不同,并以多叶型的植株、绿色的茎、疏的茎毛、倒披针型的基生叶、全缘叶、锐尖的叶尖、花色淡紫和黄色的管状花冠口等为代表性表型性状.居群内各数量性状间以单株基生叶数和单株分枝数变异系数较高(均超过50%),而花序直径变异系数最低(18.14%);居群间各表型性状以株高和单序管状花数变异系数较高(52.98%和41.98%),而单株基生叶数和基生叶长变异系数较低(<20%).地理类群间表型分化系数为26.58%,地理类群内表型分化系数为73.42%.灯盏花性状表型多样性指数以株高最高(2.243),以单株分枝数和单株基生叶数较低(1.723和1.874),总体平均表型多样性指数为2.028;不同地理类群的表型多样性指数为1.589~1.890,并以楚雄地区最高,曲靖地区最低.研究发现,灯盏花种质资源具有丰富的质量和数量性状变异,多数性状的地理类群内变异大于地理类群间,且表型多样性指数相对较高,对其地理类群内变异的保护和利用对灯盏花育种具有重要的意义.     

Molecular Parallelism Underlies Convergent Highland Adaptation of Maize Landraces

Convergent phenotypic evolution provides some of the strongest evidence for adaptation. However, the extent to which recurrent phenotypic adaptation has arisen via parallelism at the molecular level remains unresolved, as does the evolutionary origin of alleles underlying such adaptation. Here, we investigate genetic mechanisms of convergent highland adaptation in maize landrace populations and evaluate the genetic sources of recurrently selected alleles. Population branch excess statistics reveal substantial evidence of parallel adaptation at the level of individual single-nucleotide polymorphism (SNPs), genes, and pathways in four independent highland maize populations. The majority of convergently selected SNPs originated via migration from a single population, most likely in the Mesoamerican highlands, while standing variation introduced by ancient gene flow was also a contributor. Polygenic adaptation analyses of quantitative traits reveal that alleles affecting flowering time are significantly associated with elevation, indicating the flowering time pathway was targeted by highland adaptation. In addition, repeatedly selected genes were significantly enriched in the flowering time pathway, indicating their significance in adapting to highland conditions. Overall, our study system represents a promising model to study convergent evolution in plants with potential applications to crop adaptation across environmental gradients.     

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome‐wide association study using high‐density SNPs

Gossypium hirsutum L. represents the largest source of textile fibre, and China is one of the largest cotton‐producing and cotton‐consuming countries in the world. To investigate the genetic architecture of the agronomic traits of upland cotton in China, a diverse and nationwide population containing 503 G. hirsutum accessions was collected for a genome‐wide association study (GWAS) on 16 agronomic traits. The accessions were planted in four places from 2012 to 2013 for phenotyping. The CottonSNP63K array and a published high‐density map based on this array were used for genotyping. The 503 G. hirsutum accessions were divided into three subpopulations based on 11 975 quantified polymorphic single‐nucleotide polymorphisms (SNPs). By comparing the genetic structure and phenotypic variation among three genetic subpopulations, seven geographic distributions and four breeding periods, we found that geographic distribution and breeding period were not the determinants of genetic structure. In addition, no obvious phenotypic differentiations were found among the three subpopulations, even though they had different genetic backgrounds. A total of 324 SNPs and 160 candidate quantitative trait loci (QTL) regions were identified as significantly associated with the 16 agronomic traits. A network was established for multieffects in QTLs and interassociations among traits. Thirty‐eight associated regions had pleiotropic effects controlling more than one trait. One candidate gene, Gh_D08G2376, was speculated to control the lint percentage (LP). This GWAS is the first report using high‐resolution SNPs in upland cotton in China to comprehensively investigate agronomic traits, and it provides a fundamental resource for cotton genetic research and breeding.     

Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping OA简

The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield‐related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker‐trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield‐related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker‐assisted selection.     

Genome-wide association and genomic prediction for yield and component traits of Miscanthus sacchariflorus

Accelerating biomass improvement is a major goal of Miscanthus breeding. The development and implementation of genomic-enabled breeding tools, like marker-assisted selection (MAS) and genomic selection, has the potential to improve the efficiency of Miscanthus breeding. The present study conducted genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across 4 years in one subtropical and three temperate locations and genotyped with 268,109 single-nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reported Miscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield-component traits in M. sacchariflorus that may facilitate marker-assisted breeding for biomass yield. Genomic prediction accuracy for the yield-related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings of M. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings of M. sacchariflorus. This study indicated that MAS and genomic prediction will likely be beneficial for conducting population-improvement of M. sacchariflorus.     

Genomic regions underlying agronomic traits in linseed （Linum usitatissimum L.） as revealed by association mapping

The extreme climate of the Canadian Prairies poses a major chal enge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core col ection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bol s per area, 1,000 seed weight, seeds per bol , start of flowering, end of flowering, plant height, plant branching, and lodging col ected from up to eight environments was used for association mapping. Based on a mixed model （principal component analysis （PCA） t kinship matrix （K））, 12 significant marker-trait associations for six agronomic traits were identi-fied. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable al eles have additive effects. None of the modern cultivars carried the five favorable al eles and the maximum number of four observed in any accessions was mostly in＆amp;nbsp;breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while il ustrating the potential for improvement through marker-assisted selection.     

Detection of favorable alleles for yield and yield components by association mapping in upland cotton

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(??lgP?>?1.30, P?<?0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci’s alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.     

Association analysis and population structure of flowering-related traits in super sweet corn inbred lines with simple sequence repeat markers

This study assessed the genetic and phenotypic variation of 90 super sweet corn inbred lines and performed association analyses of six agronomical traits using 100 simple sequence repeats (SSR), ultimately detecting 590 alleles, with an average of 5.90 alleles per locus. The average genetic diversity and Polymorphism information content values were 0.54 and 0.50, respectively. Using population structure analysis, inbred lines were divided into three major groups and one admixed group. Association analysis was performed with a general linear model using a Q-matrix (Q GLM) and a mixed linear model using Q and K-matrices (Q + K MLM). Q GLM found 33 marker-trait associations involving 20 SSR markers that were associated with six agronomic traits. Q + K MLM identified four marker-trait associations involving three markers that were associated with traits of days of tasseling (DT) and days of silking (DS). Q GLM and Q + K MLM detected four significant marker-trait associations (SMTAs), with a level of significance of P < 0.01. In overlapping SMTAs, phi051 was associated with DT, umc1708 was associated with DS, and umc2341 was associated with two traits: DT and DS. The detection of loci associated with traits in this study may provide greater opportunities to improve quality by marker-assisted selection (MAS). Finally, these results will be helpful for breeders in choosing parental lines for crossing combinations as well as markers for using MAS in super sweet corn breeding programs in Korea.     

Dissection of the genetic architecture of three seed‐quality traits and consequences for breeding in Brassica napus

Genome‐wide association studies (GWASs) combining high‐throughput genome resequencing and phenotyping can accelerate the dissection of genetic architecture and identification of genes for plant complex traits. In this study, we developed a rapeseed genomic variation map consisting of 4 542 011 SNPs and 628 666 INDELs. GWAS was performed for three seed‐quality traits, including erucic acid content (EAC), glucosinolate content (GSC) and seed oil content (SOC) using 3.82 million polymorphisms in an association panel. Six, 49 and 17 loci were detected to be associated with EAC, GSC and SOC in multiple environments, respectively. The mean total contribution of these loci in each environment was 94.1% for EAC and 87.9% for GSC, notably higher than that for SOC (40.1%). A high correlation was observed between phenotypic variance and number of favourable alleles for associated loci, which will contribute to breeding improvement by pyramiding these loci. Furthermore, candidate genes were detected underlying associated loci, based on functional polymorphisms in gene regions where sequence variation was found to correlate with phenotypic variation. Our approach was validated by detection of well‐characterized FAE1 genes at each of two major loci for EAC on chromosomes A8 and C3, along with MYB28 genes at each of three major loci for GSC on chromosomes A9, C2 and C9. Four novel candidate genes were detected by correlation between GSC and SOC and observed sequence variation, respectively. This study provides insights into the genetic architecture of three seed‐quality traits, which would be useful for genetic improvement of B. napus.     

Hybridisation‐based target enrichment of phenology genes to dissect the genetic basis of yield and adaptation in barley

Barley (Hordeum vulgare L.) is a major cereal grain widely used for livestock feed, brewing malts and human food. Grain yield is the most important breeding target for genetic improvement and largely depends on optimal timing of flowering. Little is known about the allelic diversity of genes that underlie flowering time in domesticated barley, the genetic changes that have occurred during breeding, and their impact on yield and adaptation. Here, we report a comprehensive genomic assessment of a worldwide collection of 895 barley accessions based on the targeted resequencing of phenology genes. A versatile target‐capture method was used to detect genome‐wide polymorphisms in a panel of 174 flowering time‐related genes, chosen based on prior knowledge from barley, rice and Arabidopsis thaliana. Association studies identified novel polymorphisms that accounted for observed phenotypic variation in phenology and grain yield, and explained improvements in adaptation as a result of historical breeding of Australian barley cultivars. We found that 50% of genetic variants associated with grain yield, and 67% of the plant height variation was also associated with phenology. The precise identification of favourable alleles provides a genomic basis to improve barley yield traits and to enhance adaptation for specific production areas.     

Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.

     

香椿种质生长及叶部表型性状的遗传变异分析

以84个香椿(Toona sinensis(A.Juss.)Roem.)种质为材料,对其2个生长性状和18个叶部性状(包含6个质量性状和12个数量性状)进行测定。结果显示,香椿6个叶部质量性状变异类型丰富,呈现出多态化特点,单一性状的主要表型多为1~2个。苗高、地径及叶部表型等14个数量性状在种质间的差异均达到极显著水平,且除地径外,其他性状的遗传方差分量均大于环境方差分量,表明此类性状主要受遗传控制。参试的14个数量性状的平均表型变异系数为20.35%,平均遗传变异系数为16.36%;综合表型和遗传变异系数,叶柄长度较其他性状变异大,而叶片夹角稳定性最高,各数量性状(除地径外)遗传变异系数与表型变异系数之差小于7%。香椿种质各性状间Shannon-Weaver遗传多样性指数相差不大(1.892~2.069),遗传多样性水平高,具有良好的遗传改良基础。聚类分析可将84个香椿种质分为5类,类群Ⅰ表现为生长旺盛、小比叶重型;类群Ⅱ生长较快、叶片较大;类群Ⅲ种质数量最多,属生长缓慢、大比叶重型;类群Ⅳ特征为大叶片、多叶型;类群Ⅴ为小叶片、稀叶型。研究结果表明参试香椿种质变异丰富,遗传多样性水平高,能为良种选育、遗传改良等研究提供丰富的遗传材料。     

Improving breeding efficiency in potato using molecular and quantitative genetics

Key message

Potatoes are highly heterozygous and the conventional breeding of superior germplasm is challenging, but use of a combination of MAS and EBVs can accelerate genetic gain.

Abstract

Cultivated potatoes are highly heterozygous due to their outbreeding nature, and suffer acute inbreeding depression. Modern potato cultivars also exhibit tetrasomic inheritance. Due to this genetic heterogeneity, the large number of target traits and the specific requirements of commercial cultivars, potato breeding is challenging. A conventional breeding strategy applies phenotypic recurrent selection over a number of generations, a process which can take over 10 years. Recently, major advances in genetics and molecular biology have provided breeders with molecular tools to accelerate gains for some traits. Marker-assisted selection (MAS) can be effectively used for the identification of major genes and quantitative trait loci that exhibit large effects. There are also a number of complex traits of interest, such as yield, that are influenced by a large number of genes of individual small effect where MAS will be difficult to deploy. Progeny testing and the use of pedigree in the analysis can provide effective identification of the superior genetic factors that underpin these complex traits. Recently, it has been shown that estimated breeding values (EBVs) can be developed for complex potato traits. Using a combination of MAS and EBVs for simple and complex traits can lead to a significant reduction in the length of the breeding cycle for the identification of superior germplasm.     

Comprehensive genotyping of the USA national maize inbred seed bank

Background

Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world.

Results

The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the entire genome, with the ability to detect rare alleles at high confidence levels. More than half of the SNPs in the collection are rare. Although most rare alleles have been incorporated into public temperate breeding programs, only a modest amount of the available diversity is present in the commercial germplasm. Analysis of genetic distances shows population stratification, including a small number of large clusters centered on key lines. Nevertheless, an average fixation index of 0.06 indicates moderate differentiation between the three major maize subpopulations. Linkage disequilibrium (LD) decays very rapidly, but the extent of LD is highly dependent on the particular group of germplasm and region of the genome. The utility of these data for performing genome-wide association studies was tested with two simply inherited traits and one complex trait. We identified trait associations at SNPs very close to known candidate genes for kernel color, sweet corn, and flowering time; however, results suggest that more SNPs are needed to better explore the genetic architecture of complex traits.

Conclusions

The genotypic information described here allows this publicly available panel to be exploited by researchers facing the challenges of sustainable agriculture through better knowledge of the nature of genetic diversity.     

Population development by phenotypic selection with subsequent marker-assisted selection for line extraction in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Cucumber (Cucumis sativus L.; 2n=2x=14) has a narrow genetic base, and commercial yield of US processing cucumber has plateaued in the last 15 years. Yield may be increased by altering plant architecture to produce unique early flowering (days to flower, DTF), female (gynoecious, GYN), highly branched (multiple lateral branching, MLB), long-fruited (length:diameter ratio, L:D) cultivars with diverse plant statures. The genetic map position of QTL conditioning these quantitatively inherited yield component traits is known, and linked molecular markers may have utility in marker-assisted selection (MAS) programs to increase selection efficiency, and effectiveness. Therefore, a base population (C₀), created by intermating four unique but complementary lines, was subjected to three cycles (C₁–C₃) of phenotypic (PHE) mass selection for DTF, GYN, MLB, and L:D. In tandem, two cycles of marker-assisted backcrossing for these traits began with selected C₂ progeny (C_2S) to produce families (F₁[i.e., C_2S × C_2S], and BC₁ [i.e., F₁ × C_2S]) for line extraction, and for comparative analysis of gain from selection by PHE selection, and MAS. Frequencies of marker loci were used to monitor selection-dependent changes during PHE selection, and MAS. Similar gain from selection was detected as a result of PHE selection, and MAS for MLB (~0.3 branches/cycle), and L:D (~0.1 unit increase/cycle) with concomitant changes in frequency at linked marker loci. Although genetic gain was not realized for GYN during PHE selection, the percentage of female flowers of plants subjected to MAS was increased (5.6–9.8% per cycle) depending upon the BC₁ population examined. Selection-dependent changes in frequency were also detected at marker loci linked to female sex expression during MAS. MAS operated to fix favorable alleles that were not exploited by PHE selection in this population, indicating that MAS could be applied for altering plant architecture in cucumber to improve its yield potential. The cost of publishing this paper was defrayed in part by the payment of page charges. Under postal regulations, this paper therefore must be hereby, marked advertisement solely to indicate this fact. Mention of a trade name, proprietary product, or specific equipment does not constitute a guarantee or warranty by the USDA and does not imply its approval to the exclusion of other products that may be suitable.