Maize whole-genome InDel (insertion-deletion) chip and application thereof

Abstract

The invention discloses a maize whole-genome InDel (insertion-deletion) chip and application thereof. By large-scale sequencing mining, InDel sites of maize gene expression regions and whole-genome uniformly distributed InDel sites are determined, and the Affimatrix Axiom based high-flux InDel chip is designed and comprises probes aiming at 1536 InDel sites. The maize whole-genome InDel chip can be used for creating a maize DNA fingerprint database to perform maize variety authenticity identification, maize variety identification or authentication, maize clustering analysis, maize genetic relationship analysis and germplasm resource analysis and can also be used for maize linkage map construction, gene mapping analysis and maize molecular breeding material background selection, and a wideapplication range and remarkable benefits are realized.

Description

technical field [0001] The invention belongs to the technical field of crop breeding and molecular biology, and in particular relates to a corn whole genome InDel chip and its application. Background technique [0002] Insertion / deletion (insertion-deletion, InDel) refers to the insertion or deletion of nucleotide fragments of different sizes in the sequence of the same site in the genome between close relatives or different individuals of the same species, that is, a certain site in a sequence One or more bases are inserted or deleted compared to another sequence of homology. InDel is a phenomenon in which a homologous sequence alignment produces a gap (gap), but in most cases the ancestral sequence cannot be known, and it is difficult to determine which sequence has an insertion mutation at the gap site, or which sequence has a deletion mutation, so it is generally referred to as They are insertion / deletion mutations. [0003] Molecular markers refer to heritable and det...

AI Technical Summary

Problems solved by technology

In particular, SSR markers, with their advantages of high polymorphism, multiple alleles and convenient detection, have been the mainstream markers for molecular identification of crops in my country in the past; however, due to the low distribution density of SSR markers, data sharing is difficult and difficult Realization of scale and automation limits its large-scale application in crop molecular breeding

[0004] SNP (Single Nucleotide Polymorphism, single nucleotide polymorphism), as the third generation of genetic markers, is the most abundant distribution on the genome, with dimorphism, a single SNP site mutation rate is low, easy to achieve automation and scale through chip technology , has attracted the attention of many researchers; however, the SNP chip detection platform is often expensive, and cannot take into account the high throughput of sites and high sample throughput in genotype detection

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