F1 Clones Research Articles

Novel alleles linked to brown rust resistance in sugarcane

AbstractSugarcane brown rust, caused by Puccinia melanocephala, is a severe foliar disease that occurs in almost all countries where sugarcane is grown. The main control strategy is the use of resistant cultivars. The aim of this work was to identify molecular markers linked to genomic regions associated with a novel brown rust resistance source in sugarcane. An F1 progeny of 300 clones was obtained from a cross between TUC 00–36 and RA 87–3, highly susceptible and highly resistant to brown rust, respectively. A total of 60 F1 clones with extreme phenotype, either highly susceptible or highly resistant to brown rust, were selected. This “pooled tail” population was tested for reactions to brown rust under natural infection in the field during two crop seasons and under artificial infection in the greenhouse. Whole‐genome profiling was performed by DArT‐seq technology. Phenotypic data under both conditions and 23,299 single‐nucleotide polymorphisms (SNPs) obtained from genotyping were analysed to identify markers linked to the resistance trait. Single mapping analyses and subsequent multiple regression showed that 34 SNP markers were significantly linked to resistance alleles. These SNPs jointly explained 69% and 66% of the total phenotypic variation (R2) observed for field and controlled conditions, respectively. The mapping of the 34 SNP sequences revealed that 19 markers aligned to the sugarcane genome, whereas 12 markers aligned to the sorghum genome, all grouped on chromosome 5 with some functional annotations related to vegetal defence response. These marker loci could contribute to the development of molecular tools for molecular marker‐assisted breeding.

Lager Yeast Design Through Meiotic Segregation of a Saccharomyces cerevisiae × Saccharomyces eubayanus Hybrid.

Yeasts in the lager brewing group are closely related and consequently do not exhibit significant genetic variability. Here, an artificial Saccharomyces cerevisiae × Saccharomyces eubayanus tetraploid interspecies hybrid was created by rare mating, and its ability to sporulate and produce viable gametes was exploited to generate phenotypic diversity. Four spore clones obtained from a single ascus were isolated, and their brewing-relevant phenotypes were assessed. These F1 spore clones were found to differ with respect to fermentation performance under lager brewing conditions (15°C, 15 °Plato), production of volatile aroma compounds, flocculation potential and temperature tolerance. One spore clone, selected for its rapid fermentation and acetate ester production was sporulated to produce an F2 generation, again comprised of four spore clones from a single ascus. Again, phenotypic diversity was introduced. In two of these F2 clones, the fermentation performance was maintained and acetate ester production was improved relative to the F1 parent and the original hybrid strain. Strains also performed well in comparison to a commercial lager yeast strain. Spore clones varied in ploidy and chromosome copy numbers, and faster wort fermentation was observed in strains with a higher ploidy. An F2 spore clone was also subjected to 10 consecutive wort fermentations, and single cells were isolated from the resulting yeast slurry. These isolates also exhibited variable fermentation performance and chromosome copy numbers, highlighting the instability of polyploid interspecific hybrids. These results demonstrate the value of this natural approach to increase the phenotypic diversity of lager brewing yeast strains.

Identifying genomic regions controlling ratoon stunting disease resistance in sugarcane (Saccharum spp.) clonal F1 population

The ratoon stunting disease (RSD) of sugarcane, caused by the bacterium Leifsonia xyli subsp. xyli, is one of the major concerns to sugarcane production and breeding programs worldwide. Due to no obvious external symptoms, RSD cannot be easily detected by the growers, hence has reduced the world’s sugarcane production significantly. This study aimed to identify quantitative trait loci (QTL) associated with RSD resistance and to assist in the development of linked molecular markers for marker-assisted breeding to minimize the reduction in sugarcane yield by the RSD infection. A set of 146 individuals derived from a self-crossing of CP80-1827 were evaluated for RSD resistance in a mechanically duplicated inoculated field trial from 2014 to 2017 using tissue blot immunoassay. Leveraging the genetic data and the four years phenotyping data of CP80-1827 selfing population, linkage map construction and QTL analysis were conducted based on clonal F1 and F2 mapping population types with GACD V.1.2 and IciMapping V.3.3, respectively. A total of 23 QTL associated with RSD resistance were identified, which explained 6% to 13% of the phenotypic variation with the two types of software. A total of 82 disease resistance genes were identified by searching these 23 QTL regions on their corresponding regions on the Sorghum bicolor genome (44 genes), sugarcane R570 genome (20 genes), and S. spontaneum genome (18 genes), respectively. Compared with IciMapping V.3.3, GACD V.1.2 identified more major (6 vs. 3) and stable QTL (2 vs. 0), and more disease resistance genes (51 vs. 31), indicating GACD V.1.2 (clonal F1 mapping type) is most likely to be more efficient than IciMapping (F2 mapping type) for QTL analysis of a sefling population or clonal F1 population in clonal species. The identified QTL controlling RSD resistance along with the associated SNP markers will assist sugarcane molecular breeding programs in combating this disease.

Broadening Genetic Diversity of the Japanese Potato Gene Pool

Newly developed potato varieties in Japan have never replaced existing old varieties, indicating genetic poverty in our gene pool. To broaden the genetic diversity, Andean primitive cultivated potatoes (Andigena) were used to create parental clones. A total of 184 Andigena accessions and 10 tetraploid Solanum tarijense-Andigena hybrid clones were crossed with a breeding clone 10H17. From 6939 F1 hybrid clones, 287 were selected as long-day-adapted F1 clones. From progeny evaluation using these as pollen parents crossed with Atlantic, 95 male-fertile and high-yielding F1 clones were selected (PGEL clones). The genetic relationship was evaluated using 17,947 single nucleotide polymorphism (SNP) markers, which disclosed their distinctiveness, with larger mean Euclidean distances between PGEL clones and Japanese, foreign, or all tetraploid varieties (48.0, 49.9 or 49.4, respectively) than between Japanese and foreign varieties (47.2). Thus, these PGEL clones can be used to expand genetic diversity in Japanese potato breeding populations.

Gene action and heterosis in F1 clonal progenies of cassava for β-Carotene and farmers’ preferred traits

Gene action and heterosis provides information to assist breeder for selecting and generating improved plant recombinants. This study aimed at determining the gene action of selected cassava traits. The F1 clones exhibited considerable phenotypic variability between families and offsprings. The best F1 progenies had a higher amount of β-carotene (β-C) of 6.12 mg 100 g−1 against 1.32 mg 100 g−1 of the best parent. This superiority could be attributed to the over-dominance from the recombination of additive gene action and epistasis. The general combining ability (GCA) of parents and specific combining ability (SCA) of combinations were significant for different traits, and indicating the role of additive and non-additive gene action in controlling such traits. The significant GCA for β-C and postharvest physiological deterioration (PPD) indicates the role of additive gene action. The significant SCA for cassava mosaic disease (CMD) and cassava brown streak disease (CBSD) showed a predominance of non-additive gene action. The F1 progenies from the family Mavoka x Garukunsubire expressed the highest positive heterosis for CMD, dry matter and β-C. The high positive heterosis for β-C and DMC could be linked to transgressive segregation, because one of the parents was poor combiner.

Genetic diversity and stability in starch physicochemical property traits of potato breeding lines

Cross breeding may create wider genetic variation than two parents used in hybridization, but breeding efforts towards starch quality improvement are less reported in potato. A cross was made between Zhongshu-3 and Favorita to select desired starch properties in progenies. Among 206 F1 clones with potential high yield, starch qualities such as apparent amylose content (AAC), pasting viscosity, and thermal properties were further evaluated. A wide variation was observed in different starch physicochemical indices for 206 potato accessions. Twenty clones with high/low AAC, peak viscosity and peak gelatinization temperature were selected and then grown at another location to evaluate the stability of the traits. Similar wide range of variation in the starch properties was observed. Cluster analysis based on starch properties of the 20 selected clones indicating relative stability of the starch property traits across different locations. New breeding lines identified have potential for application in food and other industries.

Multi-allelic QTL analysis of protein content in a bi-parental population of cultivated tetraploid potato

Protein content is a key quality trait for the potato starch industry. The objective of this study was to identify allele-specific quantitative trait loci (QTLs) for tuber protein content in cultivated potato (Solanum tuberosum L.) at the tetraploid level. We analysed 496 full-sib F1 clones in a 3-year field trial to dissect the complex genetic architecture of soluble tuber protein content. Genotypic data from a 60K single nucleotide polymorphism (SNP) array was used for SNP dosage scoring, constructing homologue specific linkage maps and assembly of a dense integrated chromosomal linkage map. From the integrated map, probabilistic multi-locus identity-by-descent (IBD) haplotypes (alleles) were estimated and used to detect associations between the IBD haplotypes and the phenotypic trait values. Moderate levels of trait heritability were estimated between 40 and 74% that correspond with previous studies. Our contemporary naive analysis identified potential additive QTLs on chromosomes 2, 3, 5 (top arm) and 9 across the years. Moreover, cofactor QTL analysis identified two masked QTLs on chromosomes 1 and 5 (lower arm). The QTLs on chromosomes 2, 5 (lower arm) and 9 are reported here for the first time. The QTLs that we identified on chromosomes 1, 3 and 5 (top arm) show overlap with previous studies for protein content in potato. Collectively the naive QTLs explained 12 to 17% of the phenotypic variance. The underlying alleles of the QTLs provided both positive and negative effects on the phenotype. Our work uncovers the complex genetic architecture of this trait and describes potential breeding strategies for improvement. As protein has emerged as a high-value component from industrial potato starch production, the dissection of the genetic architecture and subsequent improvement of this trait by breeding has great economic and environmental relevance.

In vitro establishment of shoot meristems of Ilex paraguariensis and identification of endophytic bacteria

Yerba mate (Ilex paraguariensis A. St.-Hil.) is a species of great economic, social and environmental importance for the southern regions of Brazil, Uruguay and Argentina. Currently the most diverse products are obtained from mate leaves, including mate tea. The objective of this study was to establish shoot meristem cultures (meristematic dome and a few primordia) of elite clones and identify the endophytic bacteria present in the explants. We tested the effect of clones (F1, F2, A03 and A07), culture media (MS, 1/2MS, 1/4MS and WPM), cytokinins (kinetin, BA and 2iP), activated charcoal (1, 2 and 3 g L−1), and disinfecting agent (sodium hypochlorite and mercuric chloride) on in vitro establishment. F1 and F2 clones were the most responsive for shoot meristem in vitro culture. WPM medium supplemented with 8.8 µM 2iP, 0.2 µM NAA and 3 g L−1 activated charcoal was the most suitable for the in vitro establishment of the F1 clone. No phytotoxic effect of the disinfectant was observed and some meristems sprouted. The isolated endophytic bacterium was identified for the first time in yerba mate as Agrobacterium larrymoorei. To conclude, we were able to establish in vitro culture of yerba mate using meristems as explants but the tissues were not free of endophytic microorganisms which could interfere with explant response.

Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization

BackgroundInterspecific hybridization is an effective strategy for germplasm innovation in sugarcane. Nobilization refers to the breeding theory of development and utilization of wild germplasm. Saccharum spontaneum is the main donor of resistance and adaptive genes in the nobilization breeding process. Chromosome transfer in sugarcane is complicated; thus, research of different inheritance patterns can provide guidance for optimal sugarcane breeding.ResultsThrough chromosome counting and genomic in situ hybridization, we found that six clones with 80 chromosomes were typical S. officinarum and four other clones with more than 80 chromosomes were interspecific hybrids between S. officinarum and S. spontaneum. These data support the classical view that S. officinarum is characterized by 2n = 80. In addition, genomic in situ hybridization showed that five F1 clones were products of a 2n + n transmission and one F1 clone was the product of an n + n transmission in clear pedigree noble hybrids between S. officinarum and S. spontaneum. Interestingly, Yacheng 75–408 and Yacheng 75–409 were the sibling lines of the F1 progeny from the same parents but with different genetic transmissions.ConclusionsThis is the first clear evidence of Loethers, Crystallina, Luohanzhe, Vietnam Niuzhe, and Nanjian Guozhe were typical S. officinarum by GISH. Furthermore, for the first time, we identified the chromosome transmission of six F1 hybrids between S. officinarum and S. spontaneum. These findings may provide a theoretical basis for germplasm innovation in sugarcane breeding and guidance for further sugarcane nobilization.

Plant Resistance to Colorado Potato Beetle (Coleoptera: Chrysomelidae) in Diploid F2 Families Derived From Crosses Between Cultivated and Wild Potato.

Colorado potato beetle, Leptinotarsa decemlineata Say (Coleoptera: Chrysomelidae), is a serious global pest of potato, Solanum tuberosum L. Management of L. decemlineata has relied heavily on insecticides, but repeated evolution of insecticide resistance has motivated the exploration and development of alternative strategies, such as plant resistance. The recent development of two diploid potato families derived from crosses between cultivated and wild potato species (S. chacoense and S. berthaultii) has provided a unique opportunity to reexamine plant traits for resistance breeding. In this 2-yr study, we surveyed select F2 clones for the induction of L. decemlineata mortality and a reduction in defoliation in no-choice feeding assays when challenged with adults and larvae from three sites in Wisconsin. We tested for an association with glandular trichome density and foliar levels of the glycoalkaloids chaconine and solanine. Several potato clones demonstrated resistance in specific feeding assays, but none excelled consistently across experiments. Mortality and defoliation generally differed significantly among L. decemlineata populations, which could be indicative of heritable variation in beetle responses to plant defenses or variation in the physiological status of the beetle populations tested. Contrary to expectations, higher trichome density increased mortality or decreased defoliation in only a few cases, and levels of mortality and defoliation were unrelated to foliar glycoalkaloid content, warranting further investigation of the defense mechanisms of resistant clones. In addition to identifying several potential L. decemlineata resistance sources, this study underscores the need to include multiple insect populations in surveys of plant resistance to this diverse pest.

Diversity of Xylella fastidiosa host suitability among siblings from a non-traditional interspecific Prunus cross

Ten F2 clones from an initial hybridization of Prunus webbii × Prunus persica cv Harrow Blood were evaluated under greenhouse conditions for their reaction to Xylella fastidiosa subsp. fastidiosa strain M23 during two growing seasons. Clonal accessions used for the study were selected on the basis of horticultural diversity, and were a small subset of trees from a large F2 population. Foliar symptoms of M23-inoculated trees were monitored weekly throughout the 20-week growth period. Clones were then sampled for bacterial titer determinations. With the exception of parental accession Harrow Blood, all clones yielded measurable titer; however, almond leaf scorch disease symptoms were never observed in five of the ten sibling clonal accessions. Vegetative bud break and bloom phenology data collected from field-grown mother trees over a 7 year period as well as leaf morphology characters of the clonal accessions were examined for associations with bacterial titers of inoculated clones using a principal components analysis. No clear associations were noted, with small sample size limiting the predictive ability of the analysis.

Construction of genetic linkage maps of ‘Fina Sodea’ clementine (Citrus clementina) and Byungkyul (C. platymamma), a Korean landrace, based on RAPD and SSR markers

In this study, genetic linkage maps were constructed for ‘Fina Sodea’ clementine (Citrus clementina) and Byungkyul (C. platymamma) using 152 F1 clones as a mapping population. Reference-guided whole-genome sequencing, using next-generation sequencing technology, along with 82 randomly amplified polymorphic DNA markers and seven genomic simple-sequence repeat (gSSR) loci, mined 41 polymorphic gSSR loci from the direct comparative analysis. The generated linkage map for ‘Fina Sodea’ clementine contained 22 markers distributed into 10 linkage groups, with a total length of 417.7 cM and an average interval of 19.0 cM. The map for Byungkyul contained 57 markers distributed into 10 linkage groups, with a total length of 684.9 cM and a smaller average interval of 12.0 cM. Comparison of shared gSSR markers between the two maps identified collinearities, such as linkage groups B3 and C7 and groups B9 and C7. The newly developed gSSR markers greatly enrich the limited amount of gSSR markers in Citrus, providing markers that can be useful for comparative mapping and other genetic studies.

Genetic inheritance of pulp colour and selected traits of cassava (Manihot esculenta Crantz) at early generation selection.

The early generation selection of cassava quantitative and qualitative traits saves breeding resources as it can shorten breeding schemes. Inheritance analysis provides important breeding information for developing new improved varieties. This study aimed at developing an F1 segregating cassava population and determining mode of gene action of pulp colour and selected traits at early generation selection (F1 seedling and clones). The 15 families exhibited significant (P < 0.05) phenotypic variation between offspring. The general combining ability (GCA) was significant for all traits except cassava brown streak disease on leaves, whereas specific combining ability (SCA) was significant for all evaluated traits. The Garukansubire and Gitamisi genotypes were the best general combiners for improving fresh storage root yield, while G1 and G2 were the best general combiners for improved carotenoid (yellow/orange pulp colour) and delayed physiological postharvest deterioration. The pulp colour had the highest GCA/SCA ratio and percent sum of squares due to GCA. The 15 F1 families exhibited essential genetic diversity for cassava improvement. The expression of most cassava traits was controlled by both additive and non-additive gene action. The study elucidated the role of dominance effects over the additive effects for the evaluated traits. However, the pulp colour was predominantly controlled by additive gene action. This implies the possibility of improving cassava through conventional breeding using recurrent selection for most traits. © 2017 Society of Chemical Industry.

The Inheritance of Yield Components and Beta Carotene Content in Sweet Potato

Analysis of the gene action exhibited by an agronomic trait in crop plants is useful in the planning of an effective plant breeding program. This study sought to establish the inheritance variance of root yield components and beta carotene content present in sweet potato clones commonly grown in Kenya. Ten contrasting parents were selected based on their beta carotene content, dry matter content and yield potential. They were planted in pots in the green house at KEPHIS-Muguga, Kenya, where they were grafted into Ipomoea setosa to boost their ability to flower. Five parents were further selected based on their ability to flower under local environmental conditions and crossed in a 5 × 5 half diallel manner. Five parents and ten F1 clones arising from this hybridization were evaluated at KALRO-Kiboko, Kenya during two rainy seasons. The field trials were laid out in a randomized complete block design of three replications. The data were scored for root yield characteristics, beta carotene and root dry matter content. Griffing Method II, Model 1 diallel was used to estimate the general and specific combining ability. Genetic variability for beta carotene and root dry matter content indicated that the two traits were controlled mostly by both additive and dominant gene actions. Heterosis gene effects were found for beta carotene and root dry matter content which would be useful in the improvement of sweet potato productivity.

Differences in egg hatching time between cyclical and obligate parthenogenetic lineages of aphids.

Many aphid species exhibit a variation in reproductive mode which is influenced by winter climate regimes, with cyclical parthenogenetic (CP) lines dominating in cold winter areas (because they produce cold-resistant eggs) and obligate parthenogenetic (OP) ones in mild winter regions (because of their parthenogenetic overwintering). Genetic studies on several aphid species have shown that the OP trait can be transmitted during sexual events involving the 2 types of lines. This genetic system could be considered as a local safeguarding mechanism for OP alleles in case severe frost would have killed all parthenogenetically overwintering individuals. However, this strategy would only be efficient in restoring local polymorphism in breeding systems if the newly hatched OP recombinants remain competitive over their CP counterparts. In this study we compared egg hatching sequences of CP and OP F1 clones from several crosses obtained for 2 cereal aphid species, Sitobion avenae (constant 5 °C, 8 h of light) and Rhopalosiphum padi (winter outdoor conditions). For S. avenae, we obtained F1 offspring from 6 crosses, involving 4 clones while in R. padi F1 were obtained from 11 crosses involving 14 clones. We showed that in both species proportions of OP clones were higher in the first half of the progeny relative to the second half. In addition, F1 OP clones hatched in the mean about a week earlier than their CP sibs, which gives them a demographic advantage at the start of the growth season. We then discussed the consequences of this fitness advantage for the maintenance and spread of the OP trait in aphid populations.

Construction of a genetic linkage map based on RAPD, AFLP, and SSR markers for tea plant (Camellia sinensis)

Based on double pseudo-testcross theory, a population of 79 F1 clones, which was derived from a crossing of two tea cultivars using a Japanese tea cultivar “Fushun” (Camellia sinensis) as female parent and a Korean tea cultivar “Kemsull” (C. sinensis) as male parent, was applied to construct a genetic linkage map with different molecular markers. Previously, 143 random amplified polymorphism DNA (RAPD) markers and 11 simple sequence repeat (SSR) loci developed from 41 decamer random primers and 60 published SSR primer pairs, respectively, were used into our mapping analysis. In the study of amplified fragment length polymorphism (AFLP), 2439 bands were generated from 27 primer combinations with an average number of 90.3 bands for each, of which 495 (20.3%) were polymorphic. The majority of those polymorphic markers segregated in accordance with Mendelian segregation ratios at p < 0.01 for 400 (80.8%) or at p < 0.05 for 382 (77.2%), of which 136 (34.0%) or 131 (34.3%) were at 3:1 segregation ratios and 264 (66.0%) or 251 (65.7%) were at 1:1 segregation ratios at p < 0.01 and p < 0.05, respectively. For developing more SSR markers, the transcriptome sequences of flowers and leaves of two parents were obtained using high throughput RNA sequencing and compared. Afterwards, 1800 potential polymorphic SSR markers were successfully developed and 296 of them were selected and experimentally validated with a subset of tea plants (including two parents and six F1 offspring), from which 75 (25.3%) were repeatably amplified and polymorphic between two parents. From that, 29 (38.7%) newly mined SSR markers were heterozygous in “Fushun” and/or “Kemsull” and showed segregant genotypes in F1 seedlings and were adoptable by JoinMap 4.0. Totally, 678 markers including 143 RAPDs, 11 public SSRs, 495 AFLPs, and 29 newly mined SSRs were conjointly used to construct a combined linkage map for tea plant. The new genetic map located 79 RAPDs, 5 public SSRs, 214 AFLPs, and 11 new SSRs developed from RNA seq technique and covered 1441.6 cM with an average distance of 4.7 cM between two adjacent markers. This map will lay a foundation for qualitative or quantitative trait loci (QTLs) analysis of important agronomic traits for tea plant in the future study.

Whole Genome Sequencing Identifies a Novel Factor Required for Secretory Granule Maturation in Tetrahymena thermophila.

Unbiased genetic approaches have a unique ability to identify novel genes associated with specific biological pathways. Thanks to next generation sequencing, forward genetic strategies can be expanded to a wider range of model organisms. The formation of secretory granules, called mucocysts, in the ciliate Tetrahymena thermophila relies, in part, on ancestral lysosomal sorting machinery, but is also likely to involve novel factors. In prior work, multiple strains with defects in mucocyst biogenesis were generated by nitrosoguanidine mutagenesis, and characterized using genetic and cell biological approaches, but the genetic lesions themselves were unknown. Here, we show that analyzing one such mutant by whole genome sequencing reveals a novel factor in mucocyst formation. Strain UC620 has both morphological and biochemical defects in mucocyst maturation—a process analogous to dense core granule maturation in animals. Illumina sequencing of a pool of UC620 F2 clones identified a missense mutation in a novel gene called MMA1 (Mucocyst maturation). The defects in UC620 were rescued by expression of a wild-type copy of MMA1, and disrupting MMA1 in an otherwise wild-type strain phenocopies UC620. The product of MMA1, characterized as a CFP-tagged copy, encodes a large soluble cytosolic protein. A small fraction of Mma1p-CFP is pelletable, which may reflect association with endosomes. The gene has no identifiable homologs except in other Tetrahymena species, and therefore represents an evolutionarily recent innovation that is required for granule maturation.

GACD: Integrated Software for Genetic Analysis in Clonal F1 and Double Cross Populations.

Clonal species are common among plants. Clonal F1 progenies are derived from the hybridization between 2 heterozygous clones. In self- and cross-pollinated species, double crosses can be made from 4 inbred lines. A clonal F1 population can be viewed as a double cross population when the linkage phase is determined. The software package GACD (Genetic Analysis of Clonal F1 and Double cross) is freely available public software, capable of building high-density linkage maps and mapping quantitative trait loci (QTL) in clonal F1 and double cross populations. Three functionalities are integrated in GACD version 1.0: binning of redundant markers (BIN); linkage map construction (CDM); and QTL mapping (CDQ). Output of BIN can be directly used as input of CDM. After adding the phenotypic data, the output of CDM can be used as input of CDQ. Thus, GACD acts as a pipeline for genetic analysis. GACD and example datasets are freely available from www.isbreeding.net.

Quantitative trait locus mapping with background control in genetic populations of clonal F1 and double cross.

In this study, we considered five categories of molecular markers in clonal F1 and double cross populations, based on the number of distinguishable alleles and the number of distinguishable genotypes at the marker locus. Using the completed linkage maps, incomplete and missing markers were imputed as fully informative markers in order to simplify the linkage mapping approaches of quantitative trait genes. Under the condition of fully informative markers, we demonstrated that dominance effect between the female and male parents in clonal F1 and double cross populations can cause the interactions between markers. We then developed an inclusive linear model that includes marker variables and marker interactions so as to completely control additive effects of the female and male parents, as well as the dominance effect between the female and male parents. The linear model was finally used for background control in inclusive composite interval mapping (ICIM) of quantitative trait locus (QTL). The efficiency of ICIM was demonstrated by extensive simulations and by comparisons with simple interval mapping, multiple‐QTL models and composite interval mapping. Finally, ICIM was applied in one actual double cross population to identify QTL on days to silking in maize.

Linkage analysis and map construction in genetic populations of clonal F1 and double cross.

In this study, we considered four categories of molecular markers based on the number of distinguishable alleles at the marker locus and the number of distinguishable genotypes in clonal F1 progenies. For two marker loci, there are nine scenarios that allow the estimation of female, male, and/or combined recombination frequencies. In a double cross population derived from four inbred lines, five categories of markers are classified and another five scenarios are present for recombination frequency estimation. Theoretical frequencies of identifiable genotypes were given for each scenario, from which the maximum likelihood estimates of one or more of the three recombination frequencies could be estimated. If there was no analytic solution, then Newton-Raphson method was used to acquire a numerical solution. We then proposed to use an algorithm in Traveling Salesman Problem to determine the marker order. Finally, we proposed a procedure to build the two haploids of the female parent and the two haploids of the male parent in clonal F1. Once the four haploids were built, clonal F1 hybrids could be exactly regarded as a double cross population. Efficiency of the proposed methods was demonstrated in simulated clonal F1 populations and one actual maize double cross. Extensive comparisons with software JoinMap4.1, OneMap, and R/qtl show that the methodology proposed in this article can build more accurate linkage maps in less time.