Quantitative Trait Loci Alleles Research Articles

Angiopoietin-2 (ANGPT2) as a candidate gene for somatic cell score in German Holstein cattle

This study evaluated the bovine angiopoietin-2 (ANGPT2) gene as a functional and positional candidate gene underlying a previously fine mapped quantitative trait locus (QTL) for somatic cell score on bovine chromosome 27. The gene product angiopoietin-2 is directly involved in the extravasation of neutrophils, making it a promising candidate to control the amount of somatic cells in milk. A total of 11 polymorphisms were identified within the gene by comparatively resequencing the entire open reading frame of the gene as well as adjacent intronic regions. Four selected variants were genotyped in the same granddaughter design used for QTL mapping and an association study was carried out applying 2 complementary approaches. A variable number of tandem repeats in intron 7 of the gene was found to be significantly associated with cell score in all approaches and explains approximately half of the QTL variance. Analysis of ANGPT2 mRNA expression in different localizations of the udder in animals putatively carrying divergent QTL alleles revealed differential expression in the udder lymph node. Together with the physiological role of angiopoietin-2, these results support a role of ANGPT2 in the genetic control of somatic cell score. Further studies are, however, needed to further underpin this hypothesis.

Fine Mapping of the SCN Resistance QTL cqSCN‐006 and cqSCN‐007 from Glycine soja PI 468916

ABSTRACTSoybean cyst nematode (SCN) (Heterodera glycines Ichinohe [HG]) is one of the most serious soybean pests [Glycine max (L.) Merr.] worldwide and resistance is controlled by quantitative trait loci (QTL). The fine mapping of new SCN resistance QTL can provide information useful for marker‐assisted selection (MAS) in breeding programs and tools for the eventual cloning of the QTL. The objective of this study was to fine map the SCN resistance QTL cqSCN‐006 and cqSCN‐007 that originated from Glycine soja Sieb. and Zucc. plant introduction (PI) 468916. The fine mapping was done by selecting plants with recombination near these genes and testing progeny of selected plants for resistance to the HG type 2.5.7 SCN isolate PA5 and with genetic markers. For cqSCN‐006, 1236 F5 plants and 1662 F6 plants were tested with simple sequence repeat (SSR) markers flanking the QTL, and the progeny from 20 recombinant plants were tested with genetic markers and for SCN resistance. This resulted in the mapping of cqSCN‐006 to a 803.4 kb interval on soybean chromosome (chr) 15. For cqSCN‐007, 1668 F5 plants were screened with flanking SSR markers, the progeny of 18 recombinant plants were tested, and cqQTL‐007 was mapped to a 146.5 kb interval on chr 18. The markers identified in this study will be useful to breeders developing SCN‐resistant cultivars and will be highly predictive for determining which plants carry the SCN resistance QTL alleles.

Lineage-specific mapping of quantitative trait loci

We present an approach for quantitative trait locus (QTL) mapping, termed as 'lineage-specific QTL mapping', for inferring allelic changes of QTL evolution along with branches in a phylogeny. We describe and analyze the simplest case: by adding a third taxon into the normal procedure of QTL mapping between pairs of taxa, such inferences can be made along lineages to a presumed common ancestor. Although comparisons of QTL maps among species can identify homology of QTLs by apparent co-location, lineage-specific mapping of QTL can classify homology into (1) orthology (shared origin of QTL) versus (2) paralogy (independent origin of QTL within resolution of map distance). In this light, we present a graphical method that identifies six modes of QTL evolution in a three taxon comparison. We then apply our model to map lineage-specific QTLs for inbreeding among three taxa of yellow monkey-flower: Mimulus guttatus and two inbreeders M. platycalyx and M. micranthus, but critically assuming outcrossing was the ancestral state. The two most common modes of homology across traits were orthologous (shared ancestry of mutation for QTL alleles). The outbreeder M. guttatus had the fewest lineage-specific QTL, in accordance with the presumed ancestry of outbreeding. Extensions of lineage-specific QTL mapping to other types of data and crosses, and to inference of ancestral QTL state, are discussed.

The Use of Combining Ability Analysis to Identify Elite Parents for Artemisia annua F1 Hybrid Production

Artemisia annua is an important medicinal crop used for the production of the anti-malarial compound artemisinin. In order to assist in the production of affordable high quality artemisinin we have carried out an A. annua breeding programme aimed at improving artemisinin concentration and biomass. Here we report on a combining ability analysis of a diallel cross to identify robust parental lines for hybrid breeding. The parental lines were selected based on a range of phenotypic traits to encourage heterosis. The general combining ability (GCA) values for the diallel parental lines correlated to the positive alleles of quantitative trait loci (QTL) in the same parents indicating the presence of beneficial alleles that contribute to parental performance. Hybrids generated from crossing specific parental lines with good GCA were identified as having an increase in both artemisinin concentration and biomass when grown either in glasshouse or experimental field trials and compared to controls. This study demonstrates that combining ability as determined by a diallel cross can be used to identify elite parents for the production of improved A. annua hybrids. Furthermore, the selection of material for breeding using this approach was found to be consistent with our QTL-based molecular breeding approach.

Paths to selection on life history loci in different natural environments across the native range of Arabidopsis thaliana

Selection on quantitative trait loci (QTL) may vary among natural environments due to differences in the genetic architecture of traits, environment-specific allelic effects or changes in the direction and magnitude of selection on specific traits. To dissect the environmental differences in selection on life history QTL across climatic regions, we grew a panel of interconnected recombinant inbred lines (RILs) of Arabidopsis thaliana in four field sites across its native European range. For each environment, we mapped QTL for growth, reproductive timing and development. Several QTL were pleiotropic across environments, three colocalizing with known functional polymorphisms in flowering time genes (CRY2, FRI and MAF2-5), but major QTL differed across field sites, showing conditional neutrality. We used structural equation models to trace selection paths from QTL to lifetime fitness in each environment. Only three QTL directly affected fruit number, measuring fitness. Most QTL had an indirect effect on fitness through their effect on bolting time or leaf length. Influence of life history traits on fitness differed dramatically across sites, resulting in different patterns of selection on reproductive timing and underlying QTL. In two oceanic field sites with high prereproductive mortality, QTL alleles contributing to early reproduction resulted in greater fruit production, conferring selective advantage, whereas alleles contributing to later reproduction resulted in larger size and higher fitness in a continental site. This demonstrates how environmental variation leads to change in both QTL effect sizes and direction of selection on traits, justifying the persistence of allelic polymorphism at life history QTL across the species range.

Association mapping for seed size and shape traits in soybean cultivars

Seed size and shape traits are closely related to seed yield and appearance quality in soybean (Glycine max L.). Previous studies were mainly derived from bi-parental segregating populations and relatively little is known about the results in soybean cultivars. In this study, 257 soybean cultivars obtained by stratified random sampling from six geographic ecotypes in China were used to carry out association mapping for these traits using information from 135 simple sequence repeat markers and an epistatic association mapping approach implemented using an empirical Bayes algorithm. In this analysis, seed size was measured by seed length (SL), width (SW) and thickness (ST), and seed shape was evaluated by seed length-to-width (SLW), length-to-thickness (SLT) and width-to-thickness (SWT) ratios, in 2008–2010. A total of 59 main-effect quantitative trait loci (QTL) and 31 QTL-by-environment interactions were identified. Among them, 25 QTL were associated simultaneously with at least two traits; 80 QTL (90 %) could be confirmed by enriched compression mixed linear model analysis; and the size for a large number of detected QTL was minor, except for qSL-5, qSW-7e, qST-5-2 and qSLW-2. According to the estimates for the allelic effects of the detected QTL, elite alleles could be mined: for example, the 307-bp allele of QTL linked to satt453 was the best for seed length. These elite alleles could be used to design parental combinations; e.g., the cross of Zhenghezhibanzi and Nannongdahuangdou might improve seed length, and the combination of cultivars Lindou10, Deqingxiangzhudou, Ninghaixiazhidou, Zhenghezhibanzi, 0803, Shangqiu7605 and 0831 might pyramid 42 elite alleles.

Evaluation of old Carpathian apple cultivars as genetic resources of resistance to fire blight (Erwinia amylovora)

In the interests of re-diversifying cultivar use in apple, one of the most important breeding aims, apart from using local cultivars in breeding, is to improve resistance to fire blight (FB). At the Corvinus University of Budapest, the investigation of Hungarian cultivars found in the Carpathian Basin as genetic resources is a major part of the apple breeding program aimed at multiple resistance. The present study, initiated in the early 2000s, evaluates the FB resistance of 31 apple cultivars. Examination of the damage to shoots and flowers, and of the correlation between them, was carried out after artificial inoculation. Two dominant SCAR markers and one SSR marker were used for the genetic analysis of the cultivars giving the best results in phenotypic analysis, in order to detect quantitative trait locus alleles coding for FB resistance. Based on the results of several years of inoculation tests, the assayed cultivars exhibited a wide range of susceptibility levels on the basis of shoot necrosis and in terms of flower damage. A positive correlation (R = 0.058, p = 0.04) was demonstrated between the susceptibility found for the two plant organs. The cultivars Szabadkai szercsika and Sikulai, which gave outstanding results both in the flower and shoot tests and in the genetic analysis, could be suitable genetic resources for resistance breeding programmes. The present work confirmed the complex polygenic nature of FB resistance and the need to identify further markers in addition to those found on linkage group (LG) 3 and LG 7.

Bone mineral density QTL at sexual maturity and end of lay

1. An F2 cross of a broiler male line and a White Leghorn layer line was used to identify quantitative trait loci (QTL) for bone density at the onset of lay and at the end of the laying period. A total of 686 measures of humeral bone density were available for analysis. 2. There was no evidence for epistasis. 3. Genome-wide significant QTL for bone density at the onset of lay were identified on chromosomes 1 (311 cM) and 8 (2 cM) and on chromosomes 1 (311 cM), 3 (57 cM) and 8 (2 cM) with a covariate for the number of yellow follicles (a proxy for the concentration of circulating oestrogen). 4. Evidence for only 4 chromosome-wide suggestive QTL were detected at the end of lay (72 weeks). 5. Analysis of the combined data confirmed two genome-wide suggestive QTL on chromosome 1 (137 and 266 cM) and on chromosomes 8 (2 cM) and 9 (10 cM) in analyses with or without the covariate. 6. Positive QTL alleles came from the broiler line with the exception of 2 suggestive QTL at the onset of lay on chromosomes 3 and 5 in an analysis with the covariate. 7. In general, QTL acted additively, except that dominant effects were identified for three suggestive QTL at the onset of lay on chromosomes 3 (57 and 187 cM) and 5 (9 cM). 8. The significant QTL in this study were at similar locations to QTL identified in a range of crosses in other publications, suggesting that they are prime candidates for the search for genes and mutations that could be used as selection criteria to improve bone strength and decrease fractures in commercial laying hens.

Quantitative trait loci for resistance to Haemonchus contortus artificial challenge in Red Maasai and Dorper sheep of East Africa

A genome-wide scan was performed to detect quantitative trait loci (QTL) for resistance to the gastrointestinal nematode Haemonchus contortus in a double backcross population of Red Maasai and Dorper sheep. The mapping population comprised six sire families, with 1026 lambs in total. The lambs were artificially challenged with H. contortus at about 6.5 months of age, and nine phenotypes were measured: fecal egg count, packed cell volume decline, two weight traits and five worm traits. A subset of the population (342 lambs) was selectively genotyped for 172 microsatellite loci covering 25 of the 26 autosomes. QTL mapping was performed for models which assumed that the QTL alleles were either fixed or segregating within each breed, combined with models with only an additive QTL effect fitted or both additive and dominance QTL effects fitted. Overall, QTL significant at the 1% chromosome-wide level were identified for 22 combinations of trait and chromosome. Of particular interest are a region of chromosome 26 with putative QTL for all nine traits and a region of chromosome 2 with putative QTL for three traits. Favorable QTL alleles for disease resistance originated in both the Red Maasai and Dorper breeds, were not always fixed within breed and had significant dominance effects in some cases. We anticipate that this study, in combination with follow-up work and other relevant studies, will help elucidate the biology of disease resistance.

Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC(2)F(3)-derived lines developed using "Elgin" as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC(3)F(3)-derived lines developed with "Williams 82" as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30% of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.

Detection of exotic QTLs controlling nitrogen stress tolerance among wild barley introgression lines

Nitrogen (N) is one of the most important plant nutrients, controlling growth and, ultimately, yield of a cultivar. Hordeum vulgare ssp. spontaneum, the wild barley progenitor of cultivated barley, is known to possess genes that can improve tolerance against biotic and abiotic stresses. A quantitative trait locus (QTL) study with two levels of N fertilization was conducted under glasshouse in order to locate wild barley alleles that improve N stress tolerance in the genetic background of an elite barley cultivar. For this, a set of 28 barley introgression lines (S42ILs), which originate from the cross ‘Scarlett’ × ‘ISR42-8’, was studied. The S42ILs, containing single or multiple wild barley introgressions, and ‘Scarlett’ were evaluated in regard to a total of 15 traits, related to morphological parameters, grain parameters as well as to carbon (C) and N content parameters. A mixed model analysis and a subsequent Dunnett test was conducted to identify S42ILs that significantly deviate from the recurrent parent ‘Scarlett’, either tested separately for each N level, or simultaneously across both N levels. In total, 65 QTLs were detected for the S42IL set. Most QTLs were found for chlorophyll content during heading (10 QTLs) and the fewest for C/N ratio of straw (1 QTL). The individual S42ILs possessed different numbers of QTLs. For S42IL-108, a maximum of eight QTLs were found whereas S42IL-145 did not show any significant difference from ‘Scarlett’. Wild barley alleles revealed decreasing effects at 32 QTLs and increasing effects at 33 QTLs. Although 25 QTLs exhibited similar effects across both N levels, 18 and 22 QTLs exhibited effects that were only detected under N0 or N1, respectively. We, thus, conclude that it may be worth to select improved barley cultivars for N stress tolerance separately under low N fertilization, rather than extrapolating trait performances from experiments carried out under standard N fertilization conditions. A number of wild barley QTL alleles improved N stress tolerance. For example, a wild barley QTL allele on chromosome 4H, present in the Hsp introgression of S42IL-119, was associated with a 13.0 % increase of thousand grain weight across both N levels and a 20 % increase under low N supply. QTLs detected in the present study were compared with those of previous field studies of the same cross and with other QTL studies in barley and other small grains. Accordance between QTL studies (QTLs showing similar effects at the same map location) is documented and discussed. Based on our study, promising wild barley QTL alleles are available in S42ILs, which can be readily utilized to select for improved N use efficiency in barley breeding.

Validation for root‐related quantitative trait locus effects of wild origin in the cultivated background of barley (Hordeum vulgare L.)

With 4 figures and 2 tablesAbstractExtensive root system plays a major role in plant’s ability to tolerate water deficit conditions. Recently, quantitative trait locus (QTL) effects of wild origin associated with natural variation of root parameters were detected on the distal arm of chromosome 5H using 301 BC2DH lines of a cross between spring barley cultivar ‘Scarlett’ and the wild barley accession ISR42‐8. Here, we report the validation of these QTL effects in the near isogenic background of ‘Scarlett’ by using introgression lines (ILs; S42IL‐126 and S42IL‐176) of the targeted region. S42IL‐126 encompasses a single wild introgression on chromosome 5H, reaching out from 145.57 to 200.12 cM, whereas S42IL‐176 harbours a major introgression on chromosome 5H from 154.37 to 234.98 cM along with three minor introgressions on chromosomes 1H, 2H and 3H. S42IL‐126, S42IL‐176, ‘Scarlett’ and ISR42‐8 were evaluated for the root‐related traits; root dry weight (RDW), root volume (RV), root length and the associated traits; shoot dry weight and change in tiller number during drought stress (ΔTIL). The phenotypic evaluations revealed contrasting root systems in both parents where ISR42‐8 inherited highly extensive fibrous roots with respect to ‘Scarlett’. Both ‘Scarlett’ and S42IL‐126 developed smaller roots and showed no variation in root parameters, indicating that the wild introgression present in S42IL‐126 does not contain QTL alleles for the above‐mentioned root traits. On the contrary, S42IL‐176 revealed remarkable trait increases in RDW, RV and ΔTIL, which are similar to the donor parent ‘ISR42‐8’. The trait increases in S42IL‐176 are presumably due to the presence of exotic alleles at the QTLs QRDW.S42IL‐1, QRV.S42IL‐1 and QΔTIL.S42IL‐1. The comparison of phenotypic data and overlapping introgressions between S42IL‐126 and S42IL‐176 suggests that these QTLs reside on chromosome 5H in the interval between 200.12 and 234.98 cM. On the basis of the magnitude of QRDW.S42IL‐1, QRV.S42IL‐1 and QΔTIL.S42IL‐1, it is likely that these QTL effects are also linked to extra introgressions of S42IL‐176 present on chromosomes 1H where a QTL effect for RDW was also detected previously at the corresponding region of the wild introgression. In future, a follow‐up study with segregating offspring which are derived from S42IL‐176 will help to ultimately quantify and map the identified QTLs. On the basis of our QTL study, S42IL‐176 can be used for positional cloning of the underlying genes as well as to improve the root parameters of cultivated varieties.

Quantitative trait loci segregating in crosses between New Hampshire and White Leghorn chicken lines: III. Fat deposition and intramuscular fat content

In this study, a genome scan was performed to detect genomic loci that affect fat deposition in white adipose tissues and muscles in 278 F (2) males of reciprocal crosses between the genetically and phenotypically extreme inbred chicken lines New Hampshire (NHI) and White Leghorn (WL77). Genome-wide highly significant quantitative trait loci (QTL) influencing fat deposition in white adipose tissues were found on GGA2 and 4. The peak QTL positions for different visceral and subcutaneous white adipose tissues were located between 41.4 and 112.4 Mb on GGA2 and between 76.2 and 78.7 Mb on GGA4, which explained 4.2-10.4% and 4.3-11.6% respectively of the phenotypic F (2) variances. Contrary to our expectations, the QTL allele descending from the lean line WL77 on GGA4 led to increased fat deposition. We suggest a transgressive action of the obesity allele only if it is not in the genetic background of the line WL77. Additional highly significant loci for subcutaneous adipose tissue mass were identified on GGA12 and 15. For intramuscular fat content, a suggestive QTL was located on GGA14. The analysed crosses provide a valuable resource for further fine mapping of fatness genes and subsequent gene discovery.

Identifying Quantitative Trait Loci Affecting Resistance to Congenital Hypothyroidism in 129+Ter/SvJcl Strain Mice

Tyrosylprotein sulfotransferase 2 (TPST2) is one of the enzymes responsible for tyrosine O-sulfation and catalyzes the sulfation of the specific tyrosine residue of thyroid stimulating hormone receptor (TSHR). Since this modification is indispensable for the activation of TSH signaling, a non-functional TPST2 mutation (Tpst2grt) in DW/J-grt mice leads to congenital hypothyroidism (CH) characterized by severe thyroid hypoplasia and dwarfism related to TSH hyporesponsiveness. Previous studies indicated that the genetic background of the 129+Ter/SvJcl (129) mouse strain ameliorates Tpst2grt-induced CH. To identify loci responsible for CH resistance in 129 mice, we performed quantitative trait locus (QTL) analysis using backcross progenies from susceptible DW/J and resistant 129 mice. We used the first principal component calculated from body weights at 5, 8 and 10 weeks as an indicator of CH, and QTL analysis mapped a major QTL showing a highly significant linkage to the distal portion of chromosome (Chr) 2; between D2Mit62 and D2Mit304, particularly close to D2Mit255. In addition, two male-specific QTLs showing statistically suggestive linkage were also detected on Chrs 4 and 18, respectively. All QTL alleles derived from the 129 strain increased resistance to growth retardation. There was also a positive correlation between recovery from thyroid hypoplasia and the presence of the 129 allele at D2Mit255 in male progenies. These results suggested that the major QTL on Chr 2 is involved in thyroid development. Moreover, since DW/J congenic strain mice carrying both a Tpst2grt mutation and 129 alleles in the major QTL show resistance to dwarfism and thyroid hypoplasia, we confirmed the presence of the resistant gene in this region, and that it is involved in thyroid development. Further genetical analysis should lead to identification of genes for CH tolerance and, from a better understanding of thyroid organogenesis and function, the subsequent development of new treatments for thyroid disorders.

Assessment of fire blight tolerance in apple based on plant inoculations with Erwinia amylovora and DNA markers

Fire blight (Erwinia amylovora) causes serious damage to pome fruit orchards, and identification of germplasm with heritable disease resistance is therefore crucial. Two dominant SCAR (sequence characterised amplified region) marker alleles (AE10-375 and GE-8019), flanking a previously identified QTL (quantitative trait locus) for resistance to fire blight on ‘Fiesta’ linkage group 7 in apple cultivars related to ‘Cox’s Orange Pippin’, were screened on 205 apple cultivars. Both marker alleles were present in 22% of the cultivars, indicating presence of the QTL allele for tolerance, and both were lacking in 25%, indicating homozygosity for absence of the QTL tolerance allele. However, 33% had only the marker allele AE10-375, while 20% had only GE-8019, suggesting that some cultivars with the dominant alleles for both of the flanking markers can carry these on separate chromosomes and may lack the QTL allele for tolerance. In 2009 and 2010, terminal shoots of greenhouse-grown grafted trees of 21 cultivars (only 20 in 2010) were inoculated with Erwinia amylovora. ‘Idared’ (susceptible) and ‘Enterprise’ (tolerant) were included as controls. Disease severity for each cultivar was expressed as percentage of necrosis in relation to entire length of shoot, and the ranking of cultivars in 2009 and 2010 was compared with a Spearman rank correlation test, P < 0.01. A relationship between presence of both flanking marker alleles for tolerance and level of fire blight tolerance was confirmed with a Mann–Whitney U-test, P < 0.01 in 2009, and P < 0.05 in 2010. A PCO (principal coordinate) analysis based on band profiles obtained with 12 SSR (simple sequence repeat) loci produced three loose clusters, two of which contained known offspring of ‘Cox’s Orange Pippin’, and one with cultivars that were either unrelated or had an unknown origin. Cases where DNA markers did not predict level of fire blight damage as expected, were, however, as common among descendants of ‘Cox’s Orange Pippin’ as among apparently unrelated cultivars. Obviously the ‘Fiesta’ LG 7 QTL has some predictive value, both for known ‘Cox’ relatives and others, but more efficient markers would be desirable for marker-assisted selection.

Identification of QTLs for Grain Traits in Rice Using Extreme Materials in Grain Size

The grain length (GL),grain width (GW),grain thickness (GT),ratio of grain length to width (RLW),and 1000-grain weight (TGW) were evaluated in Beijing.Using a BC2F2 population including 216 lines derived from a backcross combination between GSL156 with large grain (71.9 g) and Chuanqi with small grain (12.1 g).The quantitative trait loci (QTLs) for above five grain traits were identified by composite interval mapping using SSR markers.The results showed that the five grain traits exhibited a normal continuous distribution in BC2F2 population,indicating that they were quantitative traits controlled by multiple genes.A total of 28 QTLs conferring the five grain traits were detected on chromosomes 1,2,3,4,5,6,and 12,respectively.Fourteen QTLs,namely qGL3-2,qGL3-3,qGT12-1,qGT2-1,qGT5-1,qGW1-1,qGW12-1,qGW2-1,qGW5-1,qRLW3-1,qTGW12-1,qTGW2-1,qTGW3-3,and qTGW5-1,were main-effect QTLs and explained 13.70%,52.51%,21.13%,18.79%,20.92%,14.59%,18.33%,30.03%,20.05%,24.53%,13.47%,11.43%,21.30%,and 15.68% of the observed phenotypic variance,respectively.Among them,most QTLs were mapped on chromosome 3.Six QTLs had the alleles contributing to positive effect which were derived from small grain parent Chuanqi while the other 22 QTLs alleles from large grain parent GSL156.The modes of gene action were mainly additive or partial dominance.The marker interval RM7580-RM8208 on chromosome 3 was common to the three QTLs for GW,RLW,and TGW,respectively.The marker interval,RM7636-RM5812 on chromosome 2,RM3351-RM26 on chromosome 5,and RM1103-RM17 on chromosome 12,were common to the three major QTLs,which were associated with GW,GT and TGW,respectively.The eight SSR markers used in this study would be useful in molecular breeding in rice.The alleles from parent with larger grain were showed significant effects on GL,GW,GT,and TGW.

Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions

Photosynthesis is fundamental to biomass production, but sensitive to drought. To understand the genetics of leaf photosynthesis, especially under drought, upland rice cv. Haogelao, lowland rice cv. Shennong265, and 94 of their introgression lines (ILs) were studied at flowering and grain filling under drought and well-watered field conditions. Gas exchange and chlorophyll fluorescence measurements were conducted to evaluate eight photosynthetic traits. Since these traits are very sensitive to fluctuations in microclimate during measurements under field conditions, observations were adjusted for microclimatic differences through both a statistical covariant model and a physiological approach. Both approaches identified leaf-to-air vapour pressure difference as the variable influencing the traits most. Using the simple sequence repeat (SSR) linkage map for the IL population, 1–3 quantitative trait loci (QTLs) were detected per trait–stage–treatment combination, which explained between 7.0% and 30.4% of the phenotypic variance of each trait. The clustered QTLs near marker RM410 (the interval from 57.3 cM to 68.4 cM on chromosome 9) were consistent over both development stages and both drought and well-watered conditions. This QTL consistency was verified by a greenhouse experiment under a controlled environment. The alleles from the upland rice at this interval had positive effects on net photosynthetic rate, stomatal conductance, transpiration rate, quantum yield of photosystem II (PSII), and the maximum efficiency of light-adapted open PSII. However, the allele of another main QTL from upland rice was associated with increased drought sensitivity of photosynthesis. These results could potentially be used in breeding programmes through marker-assisted selection to improve drought tolerance and photosynthesis simultaneously.

Characterization of heterotic quantitative trait loci in maize by evaluation of near-isogenic lines and their crosses at two competition levels

In a previous study on a maize (Zea mays L.) population of recombinant inbreds derived from B73×H99, we identified several quantitative trait loci (QTL) for agronomic traits with high dominance-additive ratio. Then, for four of these QTL, we developed families of near-isogenic lines (NILs) homozygous either for the QTL allele from B73 (BB) or from H99 (HH); for two of these QTL, the NILs' families were produced in two different genetic backgrounds. The present study was conducted to: (1) characterize these QTL for agronomic traits and (2) verify whether their effects were influenced by the genetic background, inbreeding level and plant density (PD). The six NILs' families were tested across 3years and in three experiments at different inbreeding levels as NILs per se and their reciprocal crosses (Experiment 1), NILs crossed to related inbreds B73 and H99 (Experiment 2) and NILs crossed to four unrelated inbreds (Experiment 3). Experiment 2 was conducted at two PDs (4.5 and 9.0 plants m(-2)). Results of Experiments 1 and 2 confirmed previous findings as to QTL effects, with dominance-additive ratio superior to 1 for several traits; as a tendency, dominance effects were more pronounced in Experiment 1. The QTL effects were also confirmed in Experiment 3. The interactions involving QTL effects, families and PD were generally negligible, suggesting a certain stability of the QTL. Results emphasize the importance of dominance effects for these QTL, suggesting that they might deserve further studies, using the NILs' families and their crosses as base materials.

Short communication: Effect of mutation age on genomic predictions

Genomic selection relies on the whole-genome evaluation of single nucleotide polymorphisms (SNP), some of them linked to quantitative trait loci (QTL). Although statistical methodology has been developed for the analysis of genomic data, little is known about the performance of SNP association studies when trying to capture variability from QTL mutations of different ages. Within this context, the influence of mutation age was analyzed under a simulation design, assuming presence or absence of selection on mutant QTL alleles. Focusing on a unique chromosome with a single QTL located in the proximal end, the performance of the genomic selection analyses was evaluated in terms of standardized mean square error (MSE). For all simulation scenarios, MSE was highest for the youngest mutations. The MSE was progressively reduced with mutation age under random mating and soft selection, and reached its maximum performance with the oldest mutations. On the other hand, moderate and strong selection caused a quick reduction of the MSE from youngest mutations to mutations arising in generations 920 to 939, thus resulting in a progressive increase for older mutations. In both cases, very young mutations escaped from genomic selection analyses, releasing a relevant amount of genetic variability that could not be captured and used in genomic selection programs. This demonstrated the need for new analytical approaches to model relevant and recent sources of variation; if captured, these young mutations could substantially contribute to current breeding schemes.

Optimal use of regression models in genome‐wide association studies

The performance of linear regression models in genome-wide association studies is influenced by how marker information is parameterized in the model. Considering the impact of parameterization is especially important when using information from multiple markers to test for association. Properties of the population, such as linkage disequilibrium (LD) and allele frequencies, will also affect the ability of a model to provide statistical support for an underlying quantitative trait locus (QTL). Thus, for a given location in the genome, the relationship between population properties and model parameterization is expected to influence the performance of the model in providing evidence for the position of a QTL. As LD and allele frequencies vary throughout the genome and between populations, understanding the relationship between these properties and model parameterization is of considerable importance in order to make optimal use of available genomic data. Here, we evaluate the performance of regression-based association models using genotype and haplotype information across the full spectrum of allele frequency and LD scenarios. Genetic marker data from 200 broiler chickens were used to simulate genomic conditions by selecting individual markers to act as surrogate QTL (sQTL) and then investigating the ability of surrounding markers to estimate sQTL genotypes and provide statistical support for their location. The LD and allele frequencies of markers and sQTL are shown to have a strong effect on the performance of models relative to one another. Our results provide an indication of the best choice of model parameterization given certain scenarios of marker and QTL LD and allele frequencies. We demonstrate a clear advantage of haplotype-based models, which account for phase uncertainty over other models tested, particularly for QTL with low minor allele frequencies. We show that the greatest advantage of haplotype models over single-marker models occurs when LD between markers and the causal locus is low. Under these situations, haplotype models have a greater accuracy of predicting the location of the QTL than other models tested.