Genetic mapping and quantitative trait locus analysis of fiber quality traits using a three-parent composite population in upland cotton (Gossypium hirsutum L.)

Composite cross populations (CP) developed from three or more cultivars/lines are frequently used to improve agronomic and economic traits in crop cultivar development programs. Employing CP in linkage map construction and quantitative trait locus (QTL) mapping may increase the marker density of upland cotton (Gossypium hirsutum L.) genetic maps, exploit more adequate gene resources and facilitate marker-assisted selection (MAS). To construct a relatively high-density map and identify QTL associated with fiber quality traits in upland cotton, three elite upland cultivars/lines, Yumian 1, CRI 35 and 7,235, were used to obtain the segregating population, Yumian 1/CRI 35//Yumian 1/7,235. A genetic map containing 978 simple sequence repeat (SSR) loci and 69 linkage groups was constructed; the map spanned 4,184.4 cM, covering approximately 94.1% of the entire tetraploid cotton genome. A total of 63 QTL were detected, explaining 8.1–55.8% of the total phenotypic variance: 11 QTL for fiber elongation, 16 QTL for fiber length, 9 QTL for fiber micronaire reading, 10 QTL for fiber strength and 17 QTL for fiber length uniformity. The genetic map and QTL detected for fiber quality traits are promising for further breeding programs of upland cotton with improved fiber quality.     

玉米杂交种掖单13号的SSR连锁图谱构建与叶夹角和叶向值的QTL定位与分析

为了增加单位面积产量, 玉米育种者已经开始了更密植更紧凑株型的选育。叶夹角和叶向值是评价玉米株型的重要指标。本研究以掖478×丹340的500个F2单株为作图群体, 构建了具有138个位点的SSR标记连锁图谱, 图谱总长度为1 394.9 cM, 平均间距10.1 cM。利用397个F2：3家系对叶夹角和叶向值进行QTL定位分析, 结果表明: 叶夹角和叶向值分别检测到6和8个QTL, 累计解释表型变异41.0%和60.8%, 单个QTL的贡献率在2.9%~13.6%之间。与叶夹角和叶向值有关的基因主要作用方式为加性和部分显性。此外两个性状共检测到9对上位性互作位点, 表明上位性互作在叶夹角和叶向值的遗传中也起较重要的作用。     

Mapping genetic loci for iron deficiency chlorosis in soybean

The objective of this study was to map genes controlling iron deficiency chlorosis in two intraspecific soybean [Glycine max (L.) Merrill] populations. Chlorosis symptoms were evaluated by visual scores and spectrometric chlorophyll determinations at the V4 stage (third trifoliolate leaf fully developed) in the field in 1993, and at V2 (first trifoliolate leaf fully developed) and V4 stages in 1994. A total of 89 RFLP and 10 SSR markers in the Pride B216 x A15 population, and 82 RFLP, 14 SSR and 1 morphological I (hilum color) markers in the Anoka x A7 population were used to map quantitative trait loci (QTL) affecting iron deficiency chlorosis. QTL with minor effects were detected on six linkage groups of the Pride B216 x A15 population, suggesting a typical polygene mechanism. In contrast, in the Anoka x A7 population, one QTL contributed an average of 72.7% of the visual score variation and 68.8% of the chlorophyll concentration variation and was mapped on linkage group N. Another QTL for visual score variation, and one for chlorophyll concentration variation were detected on linkage groups A1 and I, respectively. Due to the large LOD score and major genetic effect of the QTL on linkage group N, the quantitative data was reclassified into qualitative data fitting a one major gene model according to the means of the QTL genotypic classes. The major gene was mapped in the same interval of linkage group N using both visual scores and chlorophyll concentrations, thus verifying that one major gene is involved in segregation for iron chlorosis deficiency in the Anoka x A7 population. This study supported a previous hypothesis that two separate genetic mechanisms control iron deficiency in soybean.     

QTL mapping of yield and fiber traits based on a four-way cross population in <Emphasis Type="Italic">Gossypium hirsutum</Emphasis> L.

Four-way cross (4WC) involving four different inbred lines frequently appears in the cotton breeding programs. However, linkage analysis and quantitative trait loci (QTL) mapping with molecular markers in cotton has largely been applied to populations derived from a cross between two inbred lines, and few results of QTL dissection were conducted in a 4WC population. In this study, an attempt was made to construct a linkage map and identify QTL for yield and fiber quality traits in 4WC derived from four different inbred lines in Gossypium hirsutum L. A linkage map was constructed with 285 SSR loci and one morphological locus, covering 2113.3 cM, approximately 42% of the total recombination length of the cotton genome. A total of 31 QTL with 5.1–25.8% of the total phenotypic variance explained were detected. Twenty-four common QTL across environments showed high stability, and six QTL were environment-specific. Several genomic segments affecting multiple traits were identified. The advantage of QTL mapping using a 4WC were discussed. This study presents the first example of QTL mapping using a 4WC population in upland cotton. The results presented here will enhance the understanding of the genetic basis of yield and fiber quality traits and enable further marker-assisted selection in cultivar populations in upland cotton.     

Meta-analysis of polyploid cotton QTL shows unequal contributions of subgenomes to a complex network of genes and gene clusters implicated in lint fiber development

QTL mapping experiments yield heterogeneous results due to the use of different genotypes, environments, and sampling variation. Compilation of QTL mapping results yields a more complete picture of the genetic control of a trait and reveals patterns in organization of trait variation. A total of 432 QTL mapped in one diploid and 10 tetraploid interspecific cotton populations were aligned using a reference map and depicted in a CMap resource. Early demonstrations that genes from the non-fiber-producing diploid ancestor contribute to tetraploid lint fiber genetics gain further support from multiple populations and environments and advanced-generation studies detecting QTL of small phenotypic effect. Both tetraploid subgenomes contribute QTL at largely non-homeologous locations, suggesting divergent selection acting on many corresponding genes before and/or after polyploid formation. QTL correspondence across studies was only modest, suggesting that additional QTL for the target traits remain to be discovered. Crosses between closely-related genotypes differing by single-gene mutants yield profoundly different QTL landscapes, suggesting that fiber variation involves a complex network of interacting genes. Members of the lint fiber development network appear clustered, with cluster members showing heterogeneous phenotypic effects. Meta-analysis linked to synteny-based and expression-based information provides clues about specific genes and families involved in QTL networks.     

A High Density Consensus Genetic Map of Tetraploid Cotton That Integrates Multiple Component Maps through Molecular Marker Redundancy Check

A consensus genetic map of tetraploid cotton was constructed using six high-density maps and after the integration of a sequence-based marker redundancy check. Public cotton SSR libraries (17,343 markers) were curated for sequence redundancy using 90% as a similarity cutoff. As a result, 20% of the markers (3,410) could be considered as redundant with some other markers. The marker redundancy information had been a crucial part of the map integration process, in which the six most informative interspecific Gossypium hirsutum×G. barbadense genetic maps were used for assembling a high density consensus (HDC) map for tetraploid cotton. With redundant markers being removed, the HDC map could be constructed thanks to the sufficient number of collinear non-redundant markers in common between the component maps. The HDC map consists of 8,254 loci, originating from 6,669 markers, and spans 4,070 cM, with an average of 2 loci per cM. The HDC map presents a high rate of locus duplications, as 1,292 markers among the 6,669 were mapped in more than one locus. Two thirds of the duplications are bridging homoeologous A_T and D_T chromosomes constitutive of allopolyploid cotton genome, with an average of 64 duplications per A_T/D_T chromosome pair. Sequences of 4,744 mapped markers were used for a mutual blast alignment (BBMH) with the 13 major scaffolds of the recently released Gossypium raimondii genome indicating high level of homology between the diploid D genome and the tetraploid cotton genetic map, with only a few minor possible structural rearrangements. Overall, the HDC map will serve as a valuable resource for trait QTL comparative mapping, map-based cloning of important genes, and better understanding of the genome structure and evolution of tetraploid cotton.     

Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends

Fine mapping and positional cloning will eventually improve with the anchoring of additional markers derived from genomic clones such as BACs. From 2,603 new BAC-end genomic sequences from Gossypium hirsutum Acala ‘Maxxa’, 1,316 PCR primer pairs (designated as MUSB) were designed to flank microsatellite or simple sequence repeat motif sequences. Most (1164 or 88%) MUSB primer pairs successfully amplified DNA from three species of cotton with an average of three amplicons per marker and 365 markers (21%) were polymorphic between G. hirsutum and G. barbadense. An interspecific RIL population developed from the above two entries was used to map 433 marker loci and 46 linkage groups with a genetic distance of 2,126.3 cM covering approximately 45% of the cotton genome and an average distance between two loci of 4.9 cM. Based on genome-specific chromosomes identified in G. hirsutum tetraploid (A and D), 56.9% of the coverage was located on the A subgenome while 39.7% was assigned to the D subgenome in the genetic map, suggesting that the A subgenome may be more polymorphic and recombinationally active than originally thought. The linkage groups were assigned to 23 of the 26 chromosomes. This is the first genetic map in which the linkage groups A01 and A02/D03 have been assigned to specific chromosomes. In addition the MUSB-derived markers from BAC-end sequences markers allows fine genetic and QTL mapping of important traits and for the first time provides reconciliation of the genetic and physical maps. Limited QTL analyses suggested that loci on chromosomes 2, 3, 12, 15 and 18 may affect variation in fiber quality traits. The original BAC clones containing the newly mapped MUSB that tag the QTLs provide critical DNA regions for the discovery of gene sequences involved in biological processes such as fiber development and pest resistance in cotton. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

Comparative genetic analysis of quantitative traits in sunflower ( Helianthus annuus L.) 1. QTL involved in resistance to Sclerotinia sclerotiorum and Diaporthe helianthi

Sclerotinia sclerotiorum and Diaporthe helianthi are important pathogens of sunflower ( Helianthus annuus L.). Two hundred and twenty F2-F3 families were developed from an intraspecific cross between two inbred sunflower lines XRQ and PSC8. Using this segregating population a genetic map of 19 linkage groups with 290 molecular markers covering 2,318 cM was constructed. Disease resistances were measured in field experiments during 3 years (1998, 1999 and 2000) for phomopsis and 2 years for S. sclerotiorum (1997 and 1999). QTL were detected using the interval mapping method at a LOD threshold of 3. A total of 15 QTL for each pathogen resistance were detected across several linkage groups, confirming the polygenic nature of the resistances. These QTL explained from 7 to 41% of the phenotypic variability. The QTL for phomopsis resistance, in the 3 years of tests, mapped in the same region, and this was also true for some forms of S. sclerotiorum resistance in the 2 years of tests. On linkage group 8, QTL affecting resistance to both S. sclerotiorum and D. helianthi mycelium extension on leaves colocalised, suggesting a common component in the mechanism of resistance for these two pathogens. The colocalisation of QTL and breeding for resistance to S. sclerotiorum and to D. helianthi by pyramiding QTL in sunflower are discussed.     

Genetic Mapping of Magnaporthe grisea Avirulence Gene Corresponding to Leaf and Panicle Blast Resistant QTLs in Jao Hom Nin Rice Cultivar

The avirulence characteristic of Magnaporthe grisea isolate TH16 corresponding to Jao Hom Nin (JHN) rice cultivar was studied by mapping population of 140 random ascospore progenies derived from the cross between B1-2 and TH16 isolates. Segregation analyses of the avirulence characteristic performing on JHN rice at the seedling and flowering stages were performed in this mapping population. We used the reference map of Guy11/2539 to choose microsatellite DNA markers for mapping the avirulence gene. The genetic map of this population was constructed from 39-microsatellite markers. The genetic map was spanned by covering seven chromosomes with an average distance of 11.9 cM per marker. In mapping population the distribution of pathogenic and non-pathogenic progenies on JHN rice were found to be fitted to 1 : 1 ratio for two of the rice stages, seedling and flowering stages. The Quantitative Trait Loci (QTL) analysis for avirulence genes corresponding to two rice stages were located at the same region on chromosome 2 between markers Pyms305 and Pyms435. The LOD score and percentage of phenotypic variance explained (PVE) on two rice stages were 5.01/16.69 and 6.73/20.26, respectively. These loci were designated as Avr-JHN(lb) and Avr-JHN(pb) corresponding to leaf and panicle blast characteristics. The findings of this study can be the initial step for positional cloning and identifying any function of avirulence genes corresponding to leaf and panicle blast characteristics.     

水稻叶片水势的QTL定位与候选基因分析

为探究叶片水势(LWP)相关基因在水稻(Oryza sativa)抗旱中的作用及其遗传机制,以热研2号(Nekken2)和华占(HZ)为亲本以及构建的120个重组自交系(RILs)群体为实验材料,对水稻分蘖期叶片水势进行检测,并利用前期基于高通量测序构建的分子遗传连锁图谱进行数量性状基因座(QTL)分析。结果表明,共检...     

Identification of QTL regions and SSR markers associated with resistance to reniform nematode in <Emphasis Type="Italic">Gossypium barbadense</Emphasis> L. accession GB713

The identification of molecular markers that are closely linked to gene(s) in Gossypium barbadense L. accession GB713 that confer a high level of resistance to reniform nematode (RN), Rotylenchulus reniformis Linford & Oliveira, would be very useful in cotton breeding programs. Our objectives were to determine the inheritance of RN resistance in the accession GB713, to identify SSR markers linked with RN resistance QTLs, and to map these linked markers to specific chromosomes. We grew and scored plants for RN reproduction in the P₁, P₂, F₁, F₂, BC₁P₁, and BC₁P₂ generations from the cross of GB713 × Acala Nem-X. The generation means analysis using the six generations indicated that one or more genes were involved in the RN resistance of GB713. The interspecific F₂ population of 300 plants was genotyped with SSR molecular markers that covered most of the chromosomes of Upland cotton (G. hirsutum L.). Results showed two QTLs on chromosome 21 and one QTL on chromosome 18. One QTL on chromosome 21 was at map position 168.6 (LOD 28.0) flanked by SSR markers, BNL 1551_162 and GH 132_199 at positions 154.2 and 177.3, respectively. A second QTL on chromosome 21 was at map position 182.7 (LOD 24.6) flanked by SSR markers BNL 4011_155 and BNL 3279_106 at positions 180.6 and 184.5, respectively. Our chromosome 21 map had 61 SSR markers covering 219 cM. One QTL with smaller genetic effects was localized to chromosome 18 at map position 39.6 (LOD 4.0) and flanked by SSR markers BNL 1721_178 and BNL 569_131 at positions 27.6 and 42.9, respectively. The two QTLs on chromosome 21 had significant additive and dominance effects, which were about equal for each QTL. The QTL on chromosome 18 showed larger additive than dominance effects. Following the precedent set by the naming of the G. longicalyx Hutchinson & Lee and G. aridum [(Rose & Standley) Skovsted] sources of resistance, we suggest the usage of Ren ^barb1 and Ren ^barb2 to designate these QTLs on chromosome 21 and Ren ^barb3 on chromosome 18.     

Quantitative trait loci mapping for yield and its components by using two immortalized populations of a heterotic hybrid in Gossypium hirsutum L.

Quantitative trait loci (QTL) mapping provides a powerful tool for unraveling the genetic basis of yield and yield components as well as heterosis in upland cotton. In this research, a molecular linkage map of Xiangzamian 2 (Gossypium hirsutum L.)-derived recombinant inbred lines (RILs) was reconstructed based on increased expressed sequence tag–simple sequence repeat markers. Both the RILs and immortalized F2s (IF2) developed through intermating between RILs were grown under multiple environments. Yield and yield components including seed-cotton yield, lint yield, bolls/plant, boll weight, lint percentage, seed index, lint index and fruit branch number were measured and their QTL were repeatedly identified across environments by the composite interval mapping (CIM) method. From a total of 111 non-redundant QTL, 23 were detected in both two populations. In the meantime, multi-marker joint analyses showed that 16 of these QTL had significant environmental interaction. QTL for correlated traits tended to be collocated and most of the QTL for seed-cotton yield and lint yield were associated with QTL for at least one yield component, consistent with the results observed in correlation analyses. For many QTL with significant additive effects, positive alleles from CRI12, the inferior parent with lower yield performance, were associated with trait improvement. Trait performance of IF2s and the large number of QTL with positive dominant effects implied that dominance plays an important role in the genetic basis of heterosis in Xiangzamian 2 and that non-additive inheritance is also an important genetic mode for lint percentage in the population. These QTL can provide the bases for marker-assisted breeding programs of upland cotton.     

Distribution of genomic regions differentiating oak species assessed by QTL detection

Pedunculate oak and sessile oak are two sympatric interfertile species that exhibit leaf morphological differences. We aimed to detect quantitative trait loci (QTLs) of these traits in order to locate genomic regions involved in species differentiation. A total of 15 leaf morphological traits were assessed in a mixed forest stand composed of Quercus petraea and Q. robur and in a full-sib pedigree of Q. robur. The progeny of the full-sib family were vegetatively propagated in two successive experiments comprising 174 and 216 sibs, and assessments were made on two leaves collected on each of the 1080 and 1530 cuttings corresponding to the two experiments. Traits that exhibited strong species differences in the mixed stand tended also to have higher repeatability values in the mapping population, thus indicating higher genetic control. A genetic map was constructed for QTL detection. Composite interval mapping with the one QTL model was used for QTL detection. From one to three QTLs were detected for 13 traits. In-depth analysis of the QTLs, controlling the five morphological traits that exhibited the highest interspecific differences in the mixed stand, indicated that they were distributed on six linkage groups, with two clusters comprising QTLs of at least two discriminant traits. These results were reinforced when error 1 for QTL detection was set at 5% at the chromosome level, as up to nine clusters could be identified. In conclusion, traits involved in interspecific differentiation of oaks are under polygenic control and widespread in clusters across the genome.     

A genetic linkage map of water yam ( Dioscorea alata L.) based on AFLP markers and QTL analysis for anthracnose resistance

A genetic linkage map of the tetraploid water yam (Dioscorea alata L.) genome was constructed based on 469 co-dominantly scored amplified fragment length polymorphism (AFLP) markers segregating in an intraspecific F₁ cross. The F₁ was obtained by crossing two improved breeding lines, TDa 95/00328 as female parent and TDa 87/01091 as male parent. Since the mapping population was an F₁ cross between presumed heterozygous parents, marker segregation data from both parents were initially split into maternal and paternal data sets, and separate genetic linkage maps were constructed. Later, data analysis showed that this was not necessary and thus the combined markers from both parents were used to construct a genetic linkage map. The 469 markers were mapped on 20 linkage groups with a total map length of 1,233 cM and a mean marker spacing of 2.62 cM. The markers segregated like a diploid cross-pollinator population suggesting that the water yam genome is allo-tetraploid (2n = 4x = 40). QTL mapping revealed one AFLP marker E-14/M52-307 located on linkage group 2 that was associated with anthracnose resistance, explaining 10% of the total phenotypic variance. This map covers 65% of the yam genome and is the first linkage map reported for D. alata. The map provides a tool for further genetic analysis of traits of agronomic importance and for using marker-assisted selection in D. alata breeding programmes. QTL mapping opens new avenues for accumulating anthracnose resistance genes in preferred D. alata cultivars.     

Construction of a comprehensive PCR-based marker linkage map and QTL mapping for fiber quality traits in upland cotton (Gossypium hirsutum L.)

To facilitate marker assisted selection, there is an urgent need to construct a saturated genetic map of upland cotton (Gossypium hirsutum L.). Four types of markers including SSR, SRAP, morphological marker, and intron targeted intron–exon splice junction (IT-ISJ) marker were used to construct a linkage map with 270 F_2:7 recombinant inbred lines derived from an upland cotton cross (T586 × Yumian 1). A total of 7,508 SSR, 740 IT-ISJ and 384 SRAP primer pairs/combinations were used to screen for polymorphism between the two mapping parents, and the average polymorphisms of three types of molecular markers represented 6.8, 6.6 and 7.0%, respectively. The polymorphic primer pairs/combinations and morphological markers were used to genotype 270 recombinant inbred lines, and a map including 604 loci (509 SSR, 58 IT-ISJ, 29 SRAP and 8 morphological loci) and 60 linkage groups was constructed. The map spanned 3,140.9 cM with an average interval of 5.2 cM between two markers, approximately accounting for 70.6% of the cotton genome. Fifty-four of 60 linkage groups were ordered into 26 chromosomes. Multiple QTL mapping was used to identify QTL for fiber quality traits in five environments, and thirteen QTL were detected. These QTL included four for fiber length (FL), two for fiber strength (FS), two for fiber fineness (FF), three for fiber length uniformity (FU), and two for fiber elongation (FE), respectively. Each QTL explained between 7.4 and 43.1% of phenotypic variance. Five out of thirteen QTL (FL1 and FU1 on chromosome 6, FL2, FU2 and FF1 on chromosome7) were detected in five environments, and they explained more than 20% of the phenotypic variance. Eleven QTL were distributed on A genome, while the other two on D genome.     

Correspondence of trichome mutations in diploid and tetraploid cottons

Quantitative variation for leaf trichome number is observed within and among Gossypium species, varying from glabrous to densely pubescent phenotypes. Moreover, economically important cotton lint fibers are modified trichomes. Earlier studies have mapped quantitative trait loci (QTLs) affecting leaf pubescence in Gossypium using allotetraploids. In this study, we mapped genes responsible for leaf trichome density in a diploid A genome cross. We were able to map 3 QTLs affecting leaf pubescence based on trichome counts obtained from young leaves (YL) and mature leaves (ML). When the F(2) progeny were classified as pubescent versus glabrous, their ratio did not deviate significantly from a 3:1 model, suggesting that glabrousness is inherited in a simple Mendelian fashion. The glabrous mutation mapped to linkage group A3 at the position of major QTL YL1 and ML1 and appeared orthologous to the t1 locus of the allotetraploids. Interestingly, a fiber mutation, sma-4(ha), observed in the same F(2) population cosegregated with the glabrous marker, which indicates either close linkage or common genetic control of lint fiber and leaf trichomes. Studies of A genome diploids may help to clarify the genetic control of trichomes and fiber in both diploid and tetraploid cottons.     

Genetic characterisation of seed yield and fertility traits in perennial ryegrass (<Emphasis Type="Italic">Lolium perenne</Emphasis> L.)

Seed yield is a trait of major interest for the key grassland species Lolium perenne L. An F2 mapping population of perennial ryegrass (VrnA), recently characterised for vernalisation response, was assessed in a glasshouse for traits related to seed yield based on a lattice design with four replications over 2 years. The traits heading date, plant height, length of panicles, number of panicles per plant, seed yield per panicle, flag leaf length, flag leaf width and seed yield per plant revealed repeatabilities ranging from 41 to 76% and a considerable amount of genetic variation in the VrnA population. Path analysis partitioned the direct and indirect effects of seed yield components on seed yield per plant. Seed yield per panicle showed the highest effect on total seed yield. The adjusted mean values of each trait and a genetic linkage map consisting of 97 anonymous and 85 gene associated DNA markers were used for quantitative trait loci (QTL) analysis. Of particular interest were two QTL on linkage group (LG) 1 and LG 2, explaining 41 and 18%, respectively, of the observed phenotypic variation for the trait seed yield per panicle. Both QTL co-located with two major QTL for total seed yield per plant possibly representing the S and Z loci of the gametophytic self incompatibility (SI) system of perennial ryegrass. The diversity of SI alleles in mapping parents and the degree of heterozygosity at SI loci in the full sib progeny determines the interference of self incompatibility with seed production.     

Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL

An (Awassi × Merino) × Merino single-sire backcross family with 165 male offspring was used to map quantitative trait loci (QTL) for body composition traits on a framework map of 189 microsatellite loci across all autosomes. Two cohorts were created from the experimental progeny to represent alternative maturity classes for body composition assessment. Animals were raised under paddock conditions prior to entering the feedlot for a 90-day fattening phase. Body composition traits were derived in vivo at the end of the experiment prior to slaughter at 2 (cohort 1) and 3.5 (cohort 2) years of age, using computed tomography. Image analysis was used to gain accurate predictions for 13 traits describing major fat depots, lean muscle, bone, body proportions and body weight which were used for single- and two-QTL mapping analysis. Using a maximum-likelihood approach, three highly significant (LOD ≥ 3), 15 significant (LOD ≥ 2), and 11 suggestive QTL (1.7 ≤ LOD < 2) were detected on eleven chromosomes. Regression analysis confirmed 28 of these QTL and an additional 17 suggestive (P < 0.1) and two significant (P < 0.05) QTL were identified using this method. QTL with pleiotropic effects for two or more tissues were identified on chromosomes 1, 6, 10, 14, 16 and 23. No tissue-specific QTL were identified.A meta-assembly of ovine QTL for carcass traits from this study and public domain sources was performed and compared with a corresponding bovine meta-assembly. The assembly demonstrated QTL with effects on carcass composition in homologous regions on OAR1, 2, 6 and 21.     

Linkage analysis of molecular markers and quantitative trait loci in populations of inbred backcross lines of Brassica napus L.

Backcross populations are often used to study quantitative trait loci (QTL) after they are initially discovered in balanced populations, such as F(2), BC(1), or recombinant inbreds. While the latter are more powerful for mapping marker loci, the former have the reduced background genetic variation necessary for more precise estimation of QTL effects. Many populations of inbred backcross lines (IBLs) have been developed in plant and animal systems to permit simultaneous study and dissection of quantitative genetic variation introgressed from one source to another. Such populations have a genetic structure that can be used for linkage estimation and discovery of QTL. In this study, four populations of IBLs of oilseed Brassica napus were developed and analyzed to map genomic regions from the donor parent (a winter-type cultivar) that affect agronomic traits in spring-type inbreds and hybrids. Restriction fragment length polymorphisms (RFLPs) identified among the IBLs were used to calculate two-point recombination fractions and LOD scores through grid searches. This information allowed the enrichment of a composite genetic map of B. napus with 72 new RFLP loci. The selfed and hybrid progenies of the IBLs were evaluated during two growing seasons for several agronomic traits. Both pedigree structure and map information were incorporated into the QTL analysis by using a regression approach. The number of QTL detected for each trait and the number of effective factors calculated by using biometrical methods were of similar magnitude. Populations of IBLs were shown to be valuable for both marker mapping and QTL analysis.     

Chromosomal loci that influence oral nicotine consumption in C57BL/6J x C3H/HeJ F2 intercross mice

Several studies have demonstrated that there are genetic influences on free-choice oral nicotine consumption in mice. In order to establish the genetic architecture that underlies individual differences in free-choice nicotine consumption, quantitative trait loci (QTL) mapping was used to identify chromosomal regions that influence free-choice nicotine consumption in male and female F(2) mice derived from a cross between C57BL/6J and C3H/HeJ mice. These two mouse strains were chosen not only because they differ significantly for oral nicotine consumption, but also because they are at or near phenotypic extremes for all measures of nicotine sensitivity that have been reported. A four-bottle choice paradigm was used to assess nicotine consumption over an 8-day period. The four bottles contained water or water supplemented with 25, 50 or 100 microg/ml of nicotine base. Using micrograms of nicotine consumed per milliliter of total fluid consumed per day as the nicotine consumption phenotype, four significant QTL were identified. The QTL with the largest LOD score was located on distal chromosome 1 (peak LOD score = 15.7). Other chromosomes with significant QTL include central chromosome 4 (peak LOD score = 4.1), proximal chromosome 7 (peak LOD score = 6.1) and distal chromosome 15 (peak LOD score = 4.8). These four QTL appear to be responsible for up to 62% of the phenotypic variance in oral nicotine consumption.