Pedify

For Crop

Pedigree identify And Visualization Tools

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Samples
Heterosis Group
Tasks
Toolkit

Introduction

The crop pedigree is an important piece of information for recorded the history of lineage relatedness and genetic evolution of breeding materials, revealed the evolutionary history of crop species genera and groups within genera, clarified kinship and genetic characteristics between varieties, provide an important reference and basis for subsequent genetic improvement and cross-breeding. In order to clarify the pedigree and genetic structure of crops, here we provide a crop pedigree identify and visualization analysis algorithm (PidTools) with an integrated development of a user-friendly online analysis platform (Pidtools-WS) and a highly customizable localized and efficiently executed toolkit program. The main functions include the following
  1. Pedigree Identify: On the basis of available pedigree information or indirectly obtained using modern testing techniques, it is assumed that the parental material of the existing varieties was used in the selection and breeding process.
  2. Pedigree Structural Analysis: Parsing and reproducing the distribution of genetic fragments across parents in existing varieties based on complete genealogical information.
  3. Pedigree analysis of derived lines: Based on the original parent and related derived line data, the genetic distribution of the parent in the derived line material is resolved and visualized.

Database

In order to identify the parents of unknown lineage varieties more accurately, we have built in a sample fingerprint database consisting of genotyping data from 5791 globally important maize inbred lines of the Maize6H-60K array. After population structure analysis, these materials were divided into a total of seven groups, namely: G1(HZS), G2(YML46), G3(Mo17), G4(D340), G5(Ye478), G6(J724), G7(B73).

Pedigree Identify

Combined with a powerful genotype database, PidTools can realize accurate pedigree identify when the parentage of the sample to be tested is completely unknown, and at the same time, it supports the situation when the number of unknown parents is more than two.

Pedigree Visualization

For a clear pedigree structure, PidTools can reproduce the distribution of genetic fragments across parents on the genome, overall as well as compositional shares and recombination exchanges on each chromosome.

Pedigree analysis of derived lines

In derived line pedigree parsing, the user only needs to provide data on an important germplasm resource and its related derived lines without other parental data of these derivatives, and the algorithm parses the pedigree of these derived lines and displays them on the platform.

About US

Technical Support: Beijing Maize Seed Testing Center Software R&D room
Address: Room 108, seed building, Maize research center, Beijing academy of agricultural and forestry sciences, no.9 middle shuguang huayuan road, haidian district, Beijing
Email: holibut@gmail.com, zhangyunlongfrank@163.com
Mobile Phone: +86 13641332360, +86 15600355608
Development Teams
  1. Maize Research Center, Beijing Academy of Agriculture & Forestry Sciences (BAAFS), Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs , Shuguang Garden Middle Road No. 9, Beijing 100097, China
  2. Jilin Academy of Agricultural Sciences, Maize Research Institute, Gongzhuling 136100, China
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References

  1. Bremen, L.B., David, A.S., Portwood, J.L., Andorf, C,M., Sen, T.Z. (2019). PedigreeNet: a web-based pedigree viewer for biological databases. Bioinformatics. 35, 4184–4186.
  2. Fu, J.J., Hao, Y.F., Li, H.H., Reif, J.C., Chen, S.J., Huang, C.L., Wang, G.Y., Li, X.H., Xu, Y.B., Li, L. (2022). Integration of genomic selection with doubled-haploid evaluation in hybrid breeding: From GS 1.0 to GS 4.0 and beyond. Molecular Plant. 15, 577-580.
  3. Howard, N.P., Peace, C., Silverstein, K.A.T., Poets, A., Luby, J.J., Vanderzande, S., Durel, C.E., Muranty, H., Denancé, C., van de Weg, E. (2021). The use of shared haplotype length information for pedigree reconstruction in asexually propagated outbreeding crops, demonstrated for apple and sweet cherry. Hortic. Res. 8, 1-13.
  4. Jurado-Ruiz, F., Pradas, N., Arus, P., Aranzana, M.J. (2022). Molecular-based pedigree reconstruction of peach cultivars. Acta Hortic. 1352, 133-140.
  5. Li, C.H., Guan, H.H., Jing, X., Li, Y.Y., Wang, B.B., Li, Y.X., Liu, X.Y., Zhang, D.F., Liu, C., Xie, X.Q., et al. (2022). Genomic insights into historical improvement of heterotic groups during modern hybrid maize breeding. Nature Plants 8, 750-763.
  6. Muranty, H., Denancé, C., Feugey, L., Crépin, J., Barbier, Y., Tartarini, S., Ordidge, M., Troggio, M., Lateur, M., Nybom, H., et al. (2020). Using whole-genome SNP data to reconstruct a large multi-generation pedigree in apple germplasm. BMC Plant Biol 20, 1-18.
  7. Zhang, R.Y, Xu, G., Li, J.S., Yan, J.B., Li, H.H., Yang, X.H. (2018). Patterns of genomic variation in Chinese maize inbred lines and implications for genetic improvement. Theor Appl Genet 131, 1207–1221.
  8. Zhao, Y.K., Tian, H.L., Li, C.H., Yi, H.M., Zhang, Y.L., Li, X.H., Zhao, H., Huo, Y.X., Wang, R., Kang, D.M., et al. (2022). HTPdb and HTPtools: Exploiting maize haplotype-tag polymorphisms for germplasm resource analyses and genomics-informed breeding. Plant Communications. 3, 1-10.