Quantitative trait loci for lifespan of mated Drosophila melanogaster affect both sexes

The properties of alleles at quantitative trait loci (QTLs) contributing to variation in lifespan should be described to determine the mechanisms of evolution of life length and to predict its future changes. Previously, we and others conducted genome-wide screens for QTLs that segregate among one panel of recombinant inbred lines (RILs) using a dense molecular marker map. In non-stressful conditions, QTLs effecting the lifespans of virgin females and males were frequently sex specific. In an unrelated panel of RILs, the effects of QTLs in flies maintained in cages with mixed sexes were similar in both sexes. Here, we re-measured the lifespans of the former panel of RILs in cages with mixed sex cohorts. Lifespan declined owing to mating. The amount of decline correlated between sexes within lines. QTLs mapping to the intervals 15A-19C, 50B-57C, 63A-65A, and 96F-99B had similar effects on the lifespans of both males and females. These QTLs have previously been detected in virgin flies surveys and had sex- and/or environment-specific effects.     

The Genetic Architecture of Maize Stalk Strength

Stalk strength is an important trait in maize (Zea mays L.). Strong stalks reduce lodging and maximize harvestable yield. Studies show rind penetrometer resistance (RPR), or the force required to pierce a stalk rind with a spike, is a valid approximation of strength. We measured RPR across 4,692 recombinant inbreds (RILs) comprising the maize nested association mapping (NAM) panel derived from crosses of diverse inbreds to the inbred, B73. An intermated B73×Mo17 family (IBM) of 196 RILs and a panel of 2,453 diverse inbreds from the North Central Regional Plant Introduction Station (NCRPIS) were also evaluated. We measured RPR in three environments. Family-nested QTL were identified by joint-linkage mapping in the NAM panel. We also performed a genome-wide association study (GWAS) and genomic best linear unbiased prediction (GBLUP) in each panel. Broad sense heritability computed on a line means basis was low for RPR. Only 8 of 26 families had a heritability above 0.20. The NCRPIS diversity panel had a heritability of 0.54. Across NAM and IBM families, 18 family-nested QTL and 141 significant GWAS associations were identified for RPR. Numerous weak associations were also found in the NCRPIS diversity panel. However, few were linked to loci involved in phenylpropanoid and cellulose synthesis or vegetative phase transition. Using an identity-by-state (IBS) relationship matrix estimated from 1.6 million single nucleotide polymorphisms (SNPs) and RPR measures from 20% of the NAM panel, genomic prediction by GBLUP explained 64±2% of variation in the remaining RILs. In the NCRPIS diversity panel, an IBS matrix estimated from 681,257 SNPs and RPR measures from 20% of the panel explained 33±3% of variation in the remaining inbreds. These results indicate the high genetic complexity of stalk strength and the potential for genomic prediction to hasten its improvement.     

Survival analysis of life span quantitative trait loci in Drosophila melanogaster

We used quantitative trait loci (QTL) mapping to evaluate the age specificity of naturally segregating alleles affecting life span. Estimates of age-specific mortality rates were obtained from observing 51,778 mated males and females from a panel of 144 recombinant inbred lines (RILs). Twenty-five QTL were found, having 80 significant effects on life span and weekly mortality rates. Generation of RILs from heterozygous parents enabled us to contrast effects of QTL alleles with the means of RIL populations. Most of the low-frequency alleles increased mortality, especially at younger ages. Two QTL had negatively correlated effects on mortality at different ages, while the remainder were positively correlated. Chromosomal positions of QTL were roughly concordant with estimates from other mapping populations. Our findings are broadly consistent with a mix of transient deleterious mutations and a few polymorphisms maintained by balancing selection, which together contribute to standing genetic variation in life span.     

Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice

It has been suggested that the collaborative cross, a large set of recombinant inbred strains derived from eight inbred mouse strains, would be a powerful resource for the dissection of complex phenotypes. Here we use simulation to investigate the power of the collaborative cross to detect and map small genetic effects. We show that for a fixed population of 1000 individuals, 500 RI lines bred using a modified version of the collaborative cross design are adequate to map a single additive locus that accounts for 5% of the phenotypic variation to within 0.96 cM. In the presence of strong epistasis more strains can improve detection, but 500 lines still provide sufficient resolution to meet most goals of the collaborative cross. However, even with a very large panel of RILs, mapping resolution may not be sufficient to identify single genes unambiguously. Our results are generally applicable to the design of RILs in other species.     

Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits

The Drosophila Synthetic Population Resource (DSPR) is a newly developed multifounder advanced intercross panel consisting of >1600 recombinant inbred lines (RILs) designed for the genetic dissection of complex traits. Here, we describe the inference of the underlying mosaic founder structure for the full set of RILs from a dense set of semicodominant restriction-site-associated DNA (RAD) markers and use simulations to explore how variation in marker density and sequencing coverage affects inference. For a given sequencing effort, marker density is more important than sequence coverage per marker in terms of the amount of genetic information we can infer. We also assessed the power of the DSPR by assigning genotypes at a hidden QTL to each RIL on the basis of the inferred founder state and simulating phenotypes for different experimental designs, different genetic architectures, different sample sizes, and QTL of varying effect sizes. We found the DSPR has both high power (e.g., 84% power to detect a 5% QTL) and high mapping resolution (e.g., ～1.5 cM for a 5% QTL).     

Quantitative trait locus mapping of fitness-related traits in Drosophila melanogaster

We examined the genetic architecture of four fitness-related traits (reproductive success, ovariole number, body size and early fecundity) in a panel of 98 Oregon-R x 2b3 recombinant inbred lines (RILs). Highly significant genetic variation was observed in this population for female, but not male, reproductive success. The cross-sex genetic correlation for reproductive success was 0.20, which is not significantly different from zero. There was significant genetic variation segregating in this cross for ovariole number, but not for body size or early fecundity. The RILs were genotyped for cytological insertion sites of roo transposable elements, yielding 76 informative markers with an average spacing of 3.2 cM. Quantitative trait loci (QTL) affecting female reproductive success and ovariole number were mapped using a composite interval mapping procedure. QTL for female reproductive success were located at the tip of the X chromosome between markers at cytological locations 1B and 3E; and on the left arm of chromosome 2 in the 30D-38A cytological region. Ovariole number QTL mapped to cytological intervals 62D-69D and 98A-98E, both on the third chromosome. The regions harbouring QTL for female reproductive success and ovariole number were also identified as QTL for longevity in previous studies with these lines.     

Linkage mapping of 1454 new maize candidate gene Loci

Bioinformatic analyses of maize EST sequences have highlighted large numbers of candidate genes putatively involved in agriculturally important traits. To contribute to ongoing efforts toward mapping of these genes, we used two populations of intermated recombinant inbred lines (IRILs), which allow a higher map resolution than nonintermated RILs. The first panel (IBM), derived from B73 x Mo17, is publicly available from the Maize Genetics Cooperation Stock Center. The second panel (LHRF) was developed from F2 x F252 to map loci monomorphic on IBM. We built framework maps of 237 loci from the IBM panel and 271 loci from the LHRF panel. Both maps were used to place 1454 loci (1056 on map IBM_Gnp2004 and 398 on map LHRF_Gnp2004) that corresponded to 954 cDNA probes previously unmapped. RFLP was mostly used, but PCR-based methods were also performed for some cDNAs to map SNPs. Unlike in usual IRIL-based maps published so far, corrected meiotic centimorgan distances were calculated, taking into account the number of intermating generations undergone by the IRILs. The corrected sizes of our framework maps were 1825 cM for IBM_Gnp2004 and 1862 cM for LHRF_Gnp2004. All loci mapped on LHRF_Gnp2004 were also projected on a consensus map IBMconsensus_Gnp2004. cDNA loci formed clusters near the centromeres except for chromosomes 1 and 8.     

A large nested association mapping population for breeding and quantitative trait locus mapping in Ethiopian durum wheat

The Ethiopian plateau hosts thousands of durum wheat (Triticum turgidum subsp. durum) farmer varieties (FV) with high adaptability and breeding potential. To harness their unique allelic diversity, we produced a large nested association mapping (NAM) population intercrossing fifty Ethiopian FVs with an international elite durum wheat variety (Asassa). The Ethiopian NAM population (EtNAM) is composed of fifty interconnected bi‐parental families, totalling 6280 recombinant inbred lines (RILs) that represent both a powerful quantitative trait loci (QTL) mapping tool, and a large pre‐breeding panel. Here, we discuss the molecular and phenotypic diversity of the EtNAM founder lines, then we use an array featuring 13 000 single nucleotide polymorphisms (SNPs) to characterize a subset of 1200 EtNAM RILs from 12 families. Finally, we test the usefulness of the population by mapping phenology traits and plant height using a genome wide association (GWA) approach. EtNAM RILs showed high allelic variation and a genetic makeup combining genetic diversity from Ethiopian FVs with the international durum wheat allele pool. EtNAM SNP data were projected on the fully sequenced AB genome of wild emmer wheat, and were used to estimate pairwise linkage disequilibrium (LD) measures that reported an LD decay distance of 7.4 Mb on average, and balanced founder contributions across EtNAM families. GWA analyses identified 11 genomic loci individually affecting up to 3 days in flowering time and more than 1.6 cm in height. We argue that the EtNAM is a powerful tool to support the production of new durum wheat varieties targeting local and global agriculture.     

Variation in Cadmium Tolerance and Accumulation and Their Relationship in Wheat Recombinant Inbred Lines at Seedling Stage

In order to identify the variation of cadmium (Cd) tolerance and accumulation in wheat (Triticum aestivum L.), a study was conducted in hydroponic culture with or without Cd using recombinant inbred lines (RILs) consisting of 103 RILs derived from a cross of Chuan 35050 × Shannong 483 at seedling stage. The parameters of shoot height, secondary roots numbers, tiller numbers, shoot dry weights, root dry weights, and maximum efficiency of photosystem II photochemistry under dark-adopted conditions were measured. Cd-tolerant indexes were then calculated as relative the above traits under Cd stress to those under the control. Cd concentration in shoot or root was determined and Cd accumulation and translocation were calculated. Based on the Cd-tolerant indexes, membership function analysis was used to determine the variation of the above parameters. The results showed a continuous distribution among the RILs and then the RILs were divided into five groups according to their tolerance. Lines 76 and 17 were considered as the most Cd-tolerant lines while lines 103 and 51 were as the most Cd-sensitive lines. Meanwhile, lines 38 and 79 were with minimum Cd translocation ratio while lines 88 and 53 were with maximum Cd translocation ratio, respectively. The relationship between Cd tolerance and accumulation was not significant, indicating Cd tolerance and accumulation may be independent traits in the RILs. Thus, lines with high Cd tolerance and less Cd accumulation could be selected for wheat breeding.     

Molecular marker genotypes, heterozygosity and genetic interactions explain heterosis in Arabidopsis thaliana

The underlying mechanisms for hybrid vigor or heterosis are elusive. Here we report a population of recombinant inbred lines (RILs), derived from the two ecotypes, Col and Ler, which can serve as a permanent resource for studying the molecular basis of hybrid vigor in Arabidopsis. Using a North Carolina mating design III (NCIII), we determined the additive and dominant nature of gene action in this population. We detected heterosis among crosses of RILs with one of the two parents (Col and Ler) and analyzed genotypes and heterozygosities for RILs and test cross families (RILs crossed to Col and Ler) using a total of 446 published molecular markers. The performance of RILs and additive and dominant components in the test cross families were used to analyze QTLs for 16 traits, using QTL cartographer and composite interval mapping with 1,000 permutations for each trait. Our data suggest that locus-specific and/or genome-wide differential heterozygosity, including epistasis, plays an important role in the generation of the observed heterosis. Furthermore, the hybrid vigor occurred between two closely related ecotypes, and provides a general mechanism for novel variation generated between genetically similar materials.     

Identification of RAPD markers linked to the karnal bunt resistance genes in wheat

A set of 104 wheat recombinant inbred lines (RILs) obtained from a cross between parents resistant (HD 29) and susceptible (WH 542) to karnal bunt (KB) (caused by Neovossia indica) were screened and used to identify random amplified polymorphic DNA (RAPD) markers linked with resistance to karnal bunt as these would allow indirect marker assisted selection of KB resistant genotypes. The two parents were analysed with 92 RAPD primers. A total of 65 primers proved functional by giving scorable polymerase chain reaction (PCR) products. Of these, 21 (32 %) primers detected polymorphism between the two parental genotypes. Using these primers, bulked segregant analysis was carried out on two bulk DNAs, one obtained by pooling DNA from 10 KB resistant RILs and the other similarly derived by pooling 10 KB susceptible RILs. One marker, OPM-20 showed apparent association with resistance to KB. This was confirmed following selective genotyping of individual RILs included in the bulks.     

Natural genetic variation in cuticular hydrocarbon expression in male and female Drosophila melanogaster

Cuticular hydrocarbons (CHCs) act as contact pheromones in Drosophila melanogaster and are an important component of several ecological traits. Segregating genetic variation in the expression of CHCs at the population level in D. melanogaster is likely to be important for mate choice and climatic adaptation; however, this variation has never been characterized. Using a panel of recombinant inbred lines (RILs) derived from a natural population, we found significant between-line variation for nearly all CHCs in both sexes. We identified 25 QTL in females and 15 QTL in males that pleiotropically influence CHC expression. There was no evidence of colocalization of QTL for homologous traits across the sexes, indicating that sexual dimorphism and low intersex genetic correlations between homologous CHCs are a consequence of largely independent genetic control. This is consistent with a pattern of divergent sexual and natural selection between the sexes.     

02428×合系35的RIL群体糙米总黄酮与总生物碱含量的遗传分析

测定了水稻02428与合系35杂交培育的222个RIL(重组自交系)及其亲本的发芽糙米和糙米总黄酮和生物碱含量,对其进行遗传分析及探讨了发芽糙米和糙米中总黄酮、生物碱的含量变化.结果表明,RIL群体发芽糙米和糙米中总黄酮、生物碱呈现广泛的遗传变异,糙米总黄酮含量略高于发芽糙米,但两者均呈正态分布,类似于性状的分布特征.RIL群体发芽糙米生物碱含量是糙米的1.5倍,且两者呈偏态分布;为功能水稻的遗传及品种选育提供了一定的理论依据.     

Genotypic variation and identification of QTLs for agronomic traits,using AFLP and SSR markers in RILs of sunflower (<Emphasis Type="Italic">Helianthus annuus</Emphasis> L.)

A population of 77 recombinant inbred lines (RILs) were developed through single-seed descent from a cross between PAC-2 and RHA-266. Seeds of the above-mentioned RILs and their parents were planted in the field in a randomised complete block design with two replications. Genetic control for some agronomical traits—sowing-to-flowering date, plant height, stem diameter (SD), head diameter (HD), grain weight per plant, 1,000-grain weight (TGW) and the percentage of oil in grains—were measured for RILs and their parents. Genetic variability was observed among 77 RILs for all traits studied. Transgressive segregation occurred for some traits, and the comparison between 10% of selected RILs with the best parent showed significant difference for SD and HD as well as for TGW. A set of 123 RILs from the same cross, including the 77 above-mentioned RILs and their two parents, were screened with 409 AFLP and SSR markers, and a linkage map was constructed based on 367 markers. Several QTLs associated with the studied traits were identified. The effects of each QTL are moderate, ranging from 7% to 37%, but a high percentage of phenotypic variance is explained when considering all the covariants (TR² mean around 80% in each trait). Although the detected regions need to be more precisely mapped, the information obtained should help in marker-assisted selection.     

The Power of QTL Mapping with RILs

QTL (quantitative trait loci) mapping is commonly used to identify genetic regions responsible to important phenotype variation. A common strategy of QTL mapping is to use recombinant inbred lines (RILs), which are usually established by several generations of inbreeding of an F1 population (usually up to F6 or F7 populations). As this inbreeding process involves a large amount of labor, we are particularly interested in the effect of the number of inbreeding generations on the power of QTL mapping; a part of the labor could be saved if a smaller number of inbreeding provides sufficient power. By using simulations, we investigated the performance of QTL mapping with recombinant inbred lines (RILs). As expected, we found that the power of F4 population could be almost comparable to that of F6 and F7 populations. A potential problem in using F4 population is that a large proportion of RILs are heterozygotes. We here introduced a new method to partly relax this problem. The performance of this method was verified by simulations with a wide range of parameters including the size of the segregation population, recombination rate, genome size and the density of markers. We found our method works better than the commonly used standard method especially when there are a number of heterozygous markers. Our results imply that in most cases, QTL mapping does not necessarily require RILs at F6 or F7 generations; rather, F4 (or even F3) populations would be almost as useful as F6 or F7 populations. Because the cost to establish a number of RILs for many generations is enormous, this finding will cause a reduction in the cost of QTL mapping, thereby accelerating gene mapping in many species.     

Quantitative trait loci controlling resistance to cadmium rhizotoxicity in two recombinant inbred populations of Arabidopsis thaliana are partially shared by those for hydrogen peroxide resistance

To understand mechanisms of cadmium (Cd) tolerance variation associated with root elongation in Arabidopsis thaliana , quantitative trait loci (QTLs) and epistasis were analyzed using relative root length (RRL: % of the root length in +Cd to −Cd) as a tolerant index. Using the composite interval mapping method, three major QTLs ( P < 0.05) were detected on chromosomes 2, 4 and 5 in the recombinant inbred population derived from a cross between Landsberg erecta (L er −0) and Columbia (Col-4). The highest logarithm of odds (LOD) of 5.6 was detected with the QTL on chromosome 5 (QTL5), which is linked to the genetic marker CDPK9 and explained about 26% of the Cd tolerance variation. There was no significant difference in Cd-translocation ratio from roots to shoots between tolerant and sensitive recombinant inbreed lines (RILs), while greater accumulations of reactive oxygen species were observed in the roots of sensitive RILs. This suggested that accumulation of ROS would explain Cd tolerance variation of the L er /Col RILs, which is mainly controlled by the QTL on chromosome 5. The QTL5 in L er /Col population was also detected as one of the major QTLs controlling tolerances to hydrogen peroxide and to copper, which is another ROS generating rhizotoxic metal. The same chromosomal position was detected as a common major QTL for Cd and hydrogen peroxide tolerances in a different recombinant inbreed (RI) population derived from a cross of Col- gl1 and Kashmir (Kas-1). These data, along with a multitraits QTL analysis in both sets of RILs, suggest that peroxide damage depends on the genotype at a major Cd-tolerant locus on the upper part of chromosome 5.