1. Fingerprint construction through genotyping by sequencing for applied breeding in Brassica rapa
- Author
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Li, Guoliang, Yue, Lixin, Cai, Xu, Li, Fei, Zhang, Hui, Zhang, Shujiang, Zhang, Shifan, and Sun, Rifei
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Nucleotide sequencing -- Methods ,Rape (Plant) -- Genetic aspects ,DNA sequencing -- Methods ,Genotype -- Observations ,Biological sciences - Abstract
This study evaluated the genotyping by sequencing (GBS) protocol for fingerprinting Brassica rapa, and the data derived were more reliable than the re-sequencing data of B. rapa. Of the 10 enzyme solutions used to analyze the numbers of genotypes and single-nucleotide polymorphisms (SNPs) in B. rapa, five solutions showed better results, namely, A (HaeIII, 450-500 bp), E (RsaI+HaeIII, 500-550 bp), F (RsaI+HaeIII, 500-600 bp), G(RsaI+HaeIII, 'All' fragment), and J (RsaI+EcaRV-HF ([R]), 'All' fragment). The five enzyme solutions showed less than 40% similarity in different individuals from various samples, and 90% similarity between two individuals from one sample. The E enzyme solution was the most suitable for fingerprinting B. rapa, revealing well-distributed SNPs in the whole genome. Of the 82 highly inbred lines and 18 [F.sub.1] lines of B. rapa sequenced by GBS in the E enzyme solution, known parents of 10 [F.sub.1] lines were verified, and male parents were discovered for 8 [F.sub.1] lines that had only known female parents. This study provides a valuable method for screening parents for [F.sub.1] lines in B. rapa for the efficient evaluation of GBS with varied library construction strategies. Key wards: Brassica rapa, genotyping by sequencing, single-nucleotide polymorphisms, fingerprinting, [F.sub.1] lines, applied breeding. Cette etude a cherche a evaluer le potentiel du protocole de genotypage par sequencage (GBS) pour dresser des empreintes genetiques chez le Brassica rapa. Les donnees obtenues se sont averees plus fiables que celles derivees du re-sequencage de B. rapa. Des dix protocoles enzymatiques employes pour analyser le nombre de genotypes et de polymorphismes mono-nucleotidiques (SNP), cinq ont montre de meilleurs resultats: les protocoles A(HaeIII, 450-500 pb), E (RsaI + HaeIII, 500-550 pb), F (RsaI + HaeIII, 500-600 pb), G (RsaI + HaeIII, [much less than] Tous [much greater than]les fragments) et J (RsaI + EcoRV-HF*, [much less than] Tous [much greater than]les fragments). Les cinq protocoles enzymatiques offraient moins de 40 % de simi-larite entre individus differents et plus de 90 % de similarite entre deux individus de la meme accession. Le proto-cole E s'est avere le meilleur pour produire des empreintes genetiques chez le B. rapa, produisant des SNP bien distribues sur l'ensemble du genome. Les auteurs ont analyse 82 lignees hautement fixees et 18 [F.sub.1] du B. rapa au moyen du GBS avec le protocole E. Ils ont pu confirmer les parents connus pour 10 [F.sub.1] et les parents males ont ete identifies pour 8 [F.sub.1] dont seul le parent femelle etait connu. Cette etude fournit, au terme d'une evaluation effi-ciente de plusieurs protocoles de preparation de librairies GBS, une methode utile pour identifier les parents de [F.sub.1] chez le B. rapa dans le contexte de l'amelioration genetique. [Traduit par la Redaction] Mots-cles: Brassica rapa, genotypage par sequen^age, polymorphismes mono-nucleotidiques, [F.sub.1], selection appliquee., Introduction In the past, reference genome sequences of many crops have provided a mass of information for understanding acrop's genomic variation and genome evolution. Owing to the genome-wide abundance of [...]
- Published
- 2022
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