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CN-122012804-A - SNP molecular marker related to capsicum fruit orientation, primer set and application thereof

CN122012804ACN 122012804 ACN122012804 ACN 122012804ACN-122012804-A

Abstract

The invention provides SNP molecular markers related to the orientation of pepper fruits, a primer set and application thereof, and belongs to the technical field of molecular biological detection. The invention discloses a SNP molecular marker related to the orientation of pepper fruits, which is positioned on the 39737290 th base on chromosome 12 of the 0036143 th version of the CNA genome of the pepper, wherein the mutant base is A or G, when the genotype is AA, the orientation of the pepper fruits is downward, and when the genotype is GG or AG, the orientation of the pepper fruits is upward. The SNP molecular marker is closely related to the orientation character of the pepper fruits, the KASP detection method established based on the marker is efficient and accurate, can realize rapid identification in the seedling stage, remarkably improves the breeding selection efficiency, is simple and convenient to operate, has high flux and good stability, effectively overcomes the defects of long period and easy environmental influence of the traditional phenotype identification, and is suitable for large-scale molecular marker assisted breeding.

Inventors

  • WANG LUYAO
  • PEI HONGXIA
  • JIANG YAPING
  • Chu Fanrui
  • WANG XIYA
  • HU YURUI

Assignees

  • 浙江大学海南研究院
  • 宁夏农林科学院园艺研究所(宁夏设施农业工程技术研究中心)

Dates

Publication Date
20260512
Application Date
20260414

Claims (10)

  1. 1. A SNP molecular marker related to the orientation of pepper fruits is characterized in that the SNP molecular marker is positioned at 39737290 th base on chromosome 12 of the 0036143 th edition of pepper genome CNA, the mutant base is A or G, the orientation of the pepper fruits is downward when the genotype is AA, and the orientation of the pepper fruits is upward when the genotype is GG or AG.
  2. 2. A primer group for detecting the SNP molecular marker genotype according to claim 1, wherein the sequence of the primer group is shown as SEQ ID NO. 3-5.
  3. 3. The primer set of claim 2, wherein the primer set has a sequence of SEQ ID No.3 being a forward primer sequence F1 targeting the a allele, SEQ ID No.4 being a forward primer sequence F2 targeting the G allele, and SEQ ID No.5 being a reverse primer sequence.
  4. 4. The primer set of claim 3, wherein all forward primers are linked to a fluorescent label, which is FAM or HEX.
  5. 5. A kit for identifying the orientation of pepper fruits, characterized in that the kit comprises the primer set of any one of claims 2-4.
  6. 6. The kit of claim 5, further comprising a premix system for PCR amplification.
  7. 7. Use of the primer set according to any one of claims 2 to 4 or the kit according to any one of claims 5 to 6 for detecting the orientation of pepper fruits.
  8. 8. The application according to claim 7, characterized in that it comprises the following steps: (1) Extracting genome DNA of the capsicum; (2) Performing PCR amplification on the genomic DNA obtained in the step (1) by using the primer set according to any one of claims 2-4 or the kit according to any one of claims 5-6 to obtain a PCR amplification product; (3) And (3) carrying out genotyping detection on the PCR amplification product obtained in the step (2), wherein the genotype is AA, AG or GG, the genotype is AA, the pepper fruit is downward, and the genotype is AG or GG.
  9. 9. The use according to claim 8, wherein the PCR amplification system is 10. Mu.L in terms of FLU-ARMS 2 XPCR Mix 5. Mu.L, 10. Mu.M forward primer sequence F1.1. Mu.L, 10. Mu.M forward primer sequence F2.1. Mu.L, 10. Mu.M reverse primer sequence 0.3. Mu.L, genomic DNA 20-50 ng, ddH 2 O up to 10. Mu.L; The PCR amplification procedure was 94℃hot start 15min, 10 Touchdown cycles, 94℃20s,57℃60s for 25 cycles, 37℃read signal 60s, wherein Touchdown cycles were 94℃20s,61℃to 55.6℃60s, each cycle reduced by 0.6 ℃.
  10. 10. Use of the primer set according to any one of claims 2 to 4 or the kit according to any one of claims 5 to 6 in pepper breeding.

Description

SNP molecular marker related to capsicum fruit orientation, primer set and application thereof Technical Field The invention belongs to the technical field of molecular biology detection, and particularly relates to SNP molecular markers related to the orientation of capsicum fruits, a primer set and application thereof. Background Capsicum annuum (Capsicum spp.) is used as an important cash crop widely planted and consumed worldwide, and the morphological characteristics of fruits of the Capsicum annuum directly relate to key elements such as yield, quality, market value and the like. Among them, the orientation of capsicum fruits is a non-negligible trait. In general, the orientation of capsicum fruits can be divided into upward, downward, horizontal and other types, and the adaptability of capsicum with different orientations to illumination and ventilation conditions is different in the growth and development process, so that the growth speed, size, shape, color and other quality indexes of the fruits are affected. For example, when the pepper variety grows upwards, the pepper is more easily irradiated by light during dense planting, the synthesis of pigment in the fruits is facilitated, the color of the fruits is more vivid, but the risk of sunburn of the fruits is possibly increased due to excessive exposure to sunlight, and the pepper variety grows downwards, which is relatively more beneficial to light shading and rain prevention of the fruits and is beneficial to reducing the incidence rate of fruit diseases, but the photosynthesis efficiency and dry matter accumulation of the fruits are possibly affected to a certain extent. In traditional pepper breeding practice, improvement of fruits towards the trait mainly depends on phenotypic observation and manual selection, and the breeding cycle is long, the efficiency is low and the interference of environmental factors is large. With the rapid development of molecular biology technology, especially the application of molecular Marker Assisted Selection (MAS) technology in crop breeding, a new opportunity is brought for the precise improvement of the orientation of pepper fruits. The KASP (Kompetitive ALLELE SPECIFIC PCR) molecular marker is an emerging high-throughput, low-cost and high-precision molecular marker technology, and has great potential in the fields of plant gene positioning, variety identification, genetic improvement and the like in recent years. By designing specific primers, the method can accurately detect target genes or DNA sequences closely linked with target traits, and can rapidly and accurately screen individuals with expected fruit orientation traits at the seed or seedling stage, thereby obviously shortening the breeding period, improving the breeding efficiency and providing powerful technical support for cultivating new pepper varieties meeting market demands. However, research on KASP molecular markers of the orientation of the pepper fruits is relatively few at present, and development of efficient and stable KASP molecular markers has important practical significance and wide application prospect for promoting molecular breeding progress of the orientation of the pepper fruits. Disclosure of Invention In view of the above, the present invention aims to provide a SNP molecular marker related to the orientation of capsicum fruits, a primer set and application thereof, wherein the genotyping of capsicum fruits is achieved by detecting 39737290 th base on chromosome 12 of CNA0036143 version of capsicum genome, the mutated base is a or G, the capsicum plants of genotype AA are the capsicum plants with the capsicum fruits facing upwards, the capsicum plants of genotype AG or GG are the capsicum fruits facing downwards, the plants with specific orientations of capsicum fruits can be obtained by genotyping analysis, and molecular breeding is performed. In order to achieve the above object, the present invention provides the following technical solutions: The invention provides an SNP molecular marker related to the orientation of pepper fruits, which is positioned at 39737290 th base on chromosome 12 of the 0036143 th edition of pepper genome CNA, the mutant base is A or G, when the genotype is AA, the orientation of the pepper fruits is downward, and when the genotype is GG or AG, the orientation of the pepper fruits is upward. The invention provides a primer group for detecting the SNP molecular marker genotype, and the sequence of the primer group is shown as SEQ ID NO. 3-5. Preferably, the sequence SEQ ID NO.3 of the primer set is a forward primer sequence F1 targeting the A allele, SEQ ID NO.4 is a forward primer sequence F2 targeting the G allele, and SEQ ID NO.5 is a reverse primer sequence. Preferably, all forward primers are attached to a fluorescent label, which is FAM or HEX. The invention provides a kit for identifying the orientation of pepper fruits, which comprises the primer group. Preferably, the kit further comp