Dataset Information

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

ABSTRACT: BACKGROUND: Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard DNA and compared our data with ongoing genome and EST sequencing of domesticated conspecifics. This is the first study of its kind for waterfowl. RESULTS: More than one billion base pairs of sequence information were generated resulting in a 16× coverage of a reduced representation library of the mallard genome. Sequence reads were aligned to a draft domesticated duck reference genome and allowed for the detection of over 122,000 SNPs within our mallard sequence dataset. In addition, almost 62,000 nucleotide positions on the domesticated duck reference showed a different nucleotide compared to wild mallard. Approximately 20,000 SNPs identified within our data were shared with SNPs identified in the sequenced domestic duck or in EST sequencing projects. The shared SNPs were considered to be highly reliable and were used to benchmark non-shared SNPs for quality. Genotyping of a representative sample of 364 SNPs resulted in a SNP conversion rate of 99.7%. The correlation of the minor allele count and observed minor allele frequency in the SNP discovery pool was 0.72. CONCLUSION: We identified almost 150,000 SNPs in wild mallards that will likely yield good results in genotyping. Of these, ~101,000 SNPs were detected within our wild mallard sequences and ~49,000 were detected between wild and domesticated duck data. In the ~101,000 SNPs we found a subset of ~20,000 SNPs shared between wild mallards and the sequenced domesticated duck suggesting a low genetic divergence. Comparison of quality metrics between the total SNP set (122,000 + 62,000 = 184,000 SNPs) and the validated subset shows similar characteristics for both sets. This indicates that we have detected a large amount (~150,000) of accurately inferred mallard SNPs, which will benefit bird evolutionary studies, ecological studies (e.g. disentangling migratory connectivity) and industrial breeding programs.

SUBMITTER: Kraus RH

PROVIDER: S-EPMC3065436 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

Kraus Robert H S RH Kerstens Hindrik H D HH Van Hooft Pim P Crooijmans Richard P M A RP Van Der Poel Jan J JJ Elmberg Johan J Vignal Alain A Huang Yinhua Y Li Ning N Prins Herbert H T HH Groenen Martien A M MA

BMC genomics 20110316

<h4>Background</h4>Next generation sequencing technologies allow to obtain at low cost the genomic sequence information that currently lacks for most economically and ecologically important organisms. For the mallard duck genomic data is limited. The mallard is, besides a species of large agricultural and societal importance, also the focal species when it comes to long distance dispersal of Avian Influenza. For large scale identification of SNPs we performed Illumina sequencing of wild mallard ...[more]

PMID: 21410945

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Project description:In this study, the effect of the speed on the webbed foot locomotion of the mallard was analyzed based on a considerable number of reliable indoor test data. Four adult male mallards were selected for analysis, and the locomotion speed of the mallard was controlled using the treadmill at an accurate and adjustable speed. The locomotion pattern of the webbed foot of the mallard at different speeds was recorded using a high-speed camera. The changes in the position and conformation of the webbed foot during locomotion on a treadmill were tracked and analyzed using Simi-Motion kinematics software. The results indicated that the stride length of the mallard increased, and the stance phase duration was shortened with the increase of the speed, whereas the swing phase duration did not vary significantly. The duty factor decreased with the increase of the mallard speed but not drop below to 0.5, because the mallards flew with their wings, or moved backward relative to the treadmill with the further increase of the speed. Using the energy method to further distinguish gait, and through the percentage of congruity analysis, it was found that between 0.73 and 0.93 m/s, the gait experienced a transition from walking to grounded running, with no significant changes in spatiotemporal parameters. At speeds between 0.93 and 1.6 m/s, mallards adopt a grounded running gait. The instantaneous changes of the tarsometatarso-phalangeal joint (TMTPJ) angle and the intertarsal joint (ITJ) angle at touch-down, mid-stance and lift-off concomitant with the change of the speed were examined with the TMTPJ and ITJ angle as the research objects. Moreover, the continuous changes of the joint angles were examined in a complete stride cycle. The result indicated that the increase of the speed will also make the TMTPJ and ITJ angle change ahead of time in a stride cycle, proving the shortened stance phase duration. The ITJ angle changed much more than the TMTPJ. Thus, the above result reveals that the mallard primarily responds with the increase of the speed by adjusting the ITJ, instead of the TMTPJ. The vertical displacement of the toe joint points and the toe joint angle was studied (α joint angle is between the second toe and the third toe; β joint angle is between the third toe and the fourth toe) with a complete stride cycle as the research object. The distal phalanxes of the second, third and fourth toes first contacted the ground, and the proximal phalanx touched the ground in turn during the early stance phase duration of the mallard, as indicated by the result of this study. However, the toes got off the ground in turn from the proximal phalanxes when the mallard foot got off the ground. With the decrease of the interphalangeal α and β joint angles, the foot web tended to be close and rapidly recovered before the next touch-down. The above result reveals that the webbed foot of the mallard is a coupling system that plays a role in the adjustment of speed.

Dataset Information

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

Publications

Genome wide SNP discovery, analysis and evaluation in mallard (Anas platyrhynchos).

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