Data_Sheet_1_Live Poultry Trading Drives China's H7N9 Viral Evolution and Geographical Network Propagation.pdf

<p>The on-going reassortment, human-adapted mutations, and spillover events of novel A(H7N9) avian influenza viruses pose a significant challenge to public health in China and globally. However, our understanding of the factors that disseminate the viruses and drive their geographic distributions is limited. We applied phylogenic analysis to examine the inter-subtype interactions between H7N9 viruses and the closest H9N2 lineages in China during 2010–2014. We reconstructed and compared the inter-provincial live poultry trading and viral propagation network via phylogeographic approach and network similarity technique. The substitution rates of the isolated viruses in live poultry markets and the characteristics of localized viral evolution were also evaluated. We discovered that viral propagation was geographically-structured and followed the live poultry trading network in China, with distinct north-to-east paths of spread and circular transmission between eastern and southern regions. The epicenter of H7N9 has moved from the Shanghai–Zhejiang region to Guangdong Province was also identified. Besides, higher substitution rate was observed among isolates sampled from live poultry markets, especially for those H7N9 viruses. Live poultry trading in China may have driven the network-structured expansion of the novel H7N9 viruses. From this perspective, long-distance geographic expansion of H7N9 were dominated by live poultry movements, while at local scales, diffusion was facilitated by live poultry markets with highly-evolved viruses.</p

Chromosomal locations of QTL for kernel-related traits detected in the immortalized F₂ maize population.

<p>Note: <i>Triangle</i>, unconditional QTL for kernel length; <i>Rhombus</i>, unconditional QTL for kernel width; <i>Heart</i>, unconditional QTL for kernel volume; <i>Star</i>, unconditional QTL for kernel weight; <i>Moon</i>, conditional QTL for kernel volume; and <i>Square</i>, conditional QTL for kernel weight.</p

Correlation coefficients among five kernel-related traits in the immortalized F₂ population.

<p>Notes: ^** Significant correlation (<i>p</i>≤0.01).</p><p>Correlation coefficients for 2009 are above the diagonal, while those for 2010 are below the diagonal.</p

Performance of kernel-related traits in the immortalized F₂ population.

<p>Notes: ^a KL, kernel length; KWI, kernel width; KT, kernel thickness; KV, kernel volume; KW, kernel weight;</p>b<p>CV, coefficient of variation;</p>c<p><i>h²b</i>, broad-sense heritability;</p>d<p><i>p</i> value, statistical significance of kernel-related traits in the four environments.</p

Digenic epistatic effects detected for the five kernel-related traits in the immortalized F₂ population.

<p>Notes:^a Chr-ini is the first marker interval chromosomal location, and Chr-inj is the second marker interval chromosomal location;</p>b<p>The digenic effect of the two interacting loci; AiAj, the effect of additive-by-additive interaction between points i and j; AiDj, the effect of additive-by-dominant interaction between points i and j; DiAj, the effect of dominant-by-additive interaction between points i and j; DiDj, the effect of dominant-by-dominant interaction between points i and j; a positive or negative epistatic effect indicates that parental allele or recombinant allele combinations, respectively, increase phenotypic values;</p><p>increase phenotypic values;</p>c<p>Contribution explained by the locus pair interaction;</p>d *<p><i>p</i>≤0.0005; ^**<i>p</i>≤0.0001;</p>e<p>Bold indicates that the interval is identical to conditional or unconditional QTL.</p

Summary of the digenic epistatic analysis for the five kernel-related traits in the immortalized F₂ population.

<p>Notes: ^a The number of epistasis interactions/loci involved;</p>b<p>The number of chromosomes the loci were distributed upon;</p>c<p>The number of the corresponding epistatic interactions;</p>d<p>Contribution explained by the locus pair interaction.</p

Conditional QTL for kernel weight conditioned on the four other kernel-related traits and kernel volume conditioned on three kernel-structure characters in the immortalized F₂ population.

<p>Notes: ^a KW, kernel weight; KW|KL, kernel weight conditioned on kernel length; KW|KWI, kernel weight conditioned on kernel width; KW|KT, kernel weight conditioned on kernel thickness; KW|KV, kernel weight conditioned on kernel volume;</p>b<p>QTL, q + trait abbreviation + chromosome number + QTL number, e.g., <i>qKW7a</i>,corresponds to the first QTL for KW on chromosome 7;</p>c<p>Logarithm of odds for each QTL;</p>d<p>A, additive values (positive or negative values indicate that the additive effect was derived from Huang C or Xu 178, respectively); D, dominant values;</p>e<p>Effect of each QTL: A, additive; PD, partial dominance; D, dominance; OD, overdominance;</p>f<p>R² contribution.</p

Unconditional QTL detected for kernel-related traits in the immortalized F₂ population.

<p>Notes: ^a KL, kernel length; KWI, kernel width; KT, kernel thickness; KV, kernel volume; KW, kernel weight;</p>b<p>QTL, q + trait abbreviation + chromosome number + QTL number, e.g., <i>qKW7a</i>,corresponds to the first QTL for KW on chromosome 7;</p>c<p>Logarithm of odds for each QTL;</p>d<p>A, additive values (a positive or negative value indicates that the additive effect was derived from Huang C or Xu 178, respectively); D, dominant values;</p>e<p>Effect of each QTL: A, additive; PD, partial dominance; D, dominance;</p>f<p>R² contribution.</p

Digenic epistatic effects detected for kernel weight conditioned on four other kernel-related traits and kernel volume conditioned on three kernel-structure characteristics in the immortalized F₂ population.

<p>Notes:^a Chr-ini is the first marker interval chromosomal location, and Chr-inj is the second marker interval chromosomal location;</p>b<p>The digenic effect of the two interacting loci; AiAj, the effect of additive-by-additive interaction between points i and j; AiDj, the effect of additive-by-dominant interaction between points i and j; DiAj, the effect of dominant-by-additive interaction between points i and j; DiDj, the effect of dominant-by-dominant interaction between points i and j; a positive or negative epistatic effect indicates that the parental allele or recombinant allele combinations, respectively, increase phenotypic values;</p>c<p>Contribution explained by the locus pair interaction;</p>d *<p><i>p</i>≤0.0005; ^**<i>p</i>≤0.0001;</p>e<p>Bold indicates the interval is identical to conditional or unconditional QTL.</p