Development of GBTS and KASP Panels for Genetic Diversity, Population Structure, and Fingerprinting of a Large Collection of Broccoli (Brassica oleracea L. var. italica) in China

Optimized Pepper Target SNP-Seq Applied in Population Structure and Genetic Diversity Analysis of 496 Pepper (Capsicum spp.) Lines

Peppers are a major vegetable crop worldwide. With the completion of additional genome assemblies, a multitude of single-nucleotide polymorphisms (SNPs) can be utilized for population structure and genetic diversity analysis. In this study, we used target SNP-sequencing as a new high-throughput sequencing technology, screening out 425 perfect SNPs for analyzing the genetic diversity and population structure among 496 pepper lines from five pepper species in China and abroad. The perfect SNP panel exhibited commendable discriminative ability, as indicated by the average values of polymorphism information content, observed heterozygosity, minor allele frequency, and genetic diversity, which were 0.346, 0.011, 0.371, and 0.449, respectively. Based on phylogenetic, population structure, and principal component analyses, 484 C. annuum lines were divided into four subpopulations according to the shape of fruit: blocky fruit, wide-horn fruit, narrow-horn fruit, and linear fruit. These subpopulations displayed clear clustering with minimal or no overlap. Moreover, F statistic (Fst) analysis revealed considerable distinctions among these subpopulations. Additionally, we established a set of 47 core SNPs that could effectively differentiate among all pepper lines. This core SNP set could precisely classify the C. annuum lines into four distinct fruit-shape groups. The blocky and narrow-horn fruit subpopulations displayed the lowest and highest genetic diversity, respectively. This study highlights the importance of fruit shape as a crucial trait in pepper breeding. Moreover, this work indicates the immense potential of optimized target SNP technology in the addition of foreground markers of important traits to improve molecular breeding efficiency, and demonstrates its broad application prospects in the genetic analysis and variety identification of peppers.

Construction of SNP fingerprints and genetic diversity analysis of radish (Raphanus sativus L.)

Radish (Raphanus sativus L.) is a vegetable crop with economic value and ecological significance in the genus Radish, family Brassicaceae. In recent years, developed countries have attached great importance to the collection and conservation of radish germplasm resources and their research and utilization, but the lack of population genetic information and molecular markers has hindered the development of the genetic breeding of radish. In this study, we integrated the radish genomic data published in databases for the development of single-nucleotide polymorphism (SNP) markers, and obtained a dataset of 308 high-quality SNPs under strict selection criteria. With the support of Kompetitive Allele-Specific PCR (KASP) technology, we screened a set of 32 candidate core SNP marker sets to analyse the genetic diversity of the collected 356 radish varieties. The results showed that the mean values of polymorphism information content (PIC), minor allele frequency (MAF), gene diversity and heterozygosity of the 32 candidate core SNP markers were 0.32, 0.30, 0.40 and 0.25, respectively. Population structural analysis, principal component analysis and genetic evolutionary tree analysis indicated that the 356 radish materials were best classified into two taxa, and that the two taxa of the material were closely genetically exchanged. Finally, on the basis of 32 candidate core SNP markers we calculated 15 core markers using a computer algorithm to construct a fingerprint map of 356 radish varieties. Furthermore, we constructed a core germplasm population consisting of 71 radish materials using 32 candidate core markers. In this study, we developed SNP markers for radish cultivar identification and genetic diversity analysis, and constructed DNA fingerprints, providing a basis for the identification of radish germplasm resources and molecular marker-assisted breeding as well as genetic research.

Research progress on the utilization technology of broccoli stalk, leaf resources, and the mechanism of action of its bioactive substances

Broccoli is a nutritious vegetable. It is high in protein, minerals, and vitamins. Also, it possesses antioxidant activities and is beneficial to the human body. Due to its active effect, broccoli is widely accepted by people in daily life. However, in terms of current utilization, only its florets are consumed as vegetables, while more than half of its stalks and leaves are not utilized. The stalks and leaves contain not only nutrients but also bioactive substances with physiologically regulating properties. Therefore research into the action and mechanism of its bioactive substances as well as its development and utilization technology will make contributions to the further promotion of its resource development and utilization. As a theoretical foundation for the resource utilization of broccoli stalks and leaves, this report will review the distribution and consumption of broccoli germplasm resources, the mechanism of action of bioactive substances, and innovative methods for their exploitation.

Construction of SNP fingerprint and population genetic analysis of honeysuckle germplasm resources in China

INTRODUCTION

The flower buds of Lonicera japonica Thunb. are widely used in Chinese medicine for their anti-inflammatory properties, and they have played an important role in the fight against SARS COVID-19 and other major epidemics. However, due to the lack of scientific and accurate variety identification methods and national unified standards, scattered and non-standardized management in flower bud production has led to mixed varieties that have caused significant difficulties in the cataloging and preservation of germplasm resources and the identification, promotion, and application of new L. japonica varieties.

METHODS

In this study, we evaluated the population structure, genetic relationships, and genetic fingerprints of 39 germplasm resources of Lonicera in China using simplified genome sequencing technology.

RESULTS

A total of 13,143,268 single nucleotide polymorphisms (SNPs) were identified. Thirty-nine samples of Lonicera were divided into four subgroups, and the population structure and genetic relationships among existing Lonicera germplasm resources were determined using principal component analysis, population structure analysis, and phylogenetic tree analysis. Through several stringent selection criteria, 15 additional streamlined, high-quality DNA fingerprints were filtered out of the validated 50 SNP loci and verified as being able to effectively identify the 39 Lonicera varieties.

DISCUSSION

To our knowledge, this is the first comprehensive study measuring the diversity and population structure of a large collection of Lonicera varieties in China. These results have greatly broadened our understanding of the diversity, phylogeny, and population structure of Lonicera. The results may enhance the future analysis of genetic diversity, species identification, property rights disputes, and molecular breeding by providing a scientific basis and reference data for these efforts.

BrACOS5 mutations induced male sterility via impeding pollen exine formation in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

BrACOS5 mutations led to male sterility of Chinese cabbage verified in three allelic male-sterile mutants. Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the major vegetable crops in East Asia, and the utilization of male-sterile line is an important measure for its hybrid seed production. Herein, we isolated three allelic male-sterile mutants, msm1-1, msm1-2 and msm1-3, from an ethyl methane sulfonate (EMS) mutagenized population of Chinese cabbage double-haploid (DH) line 'FT', whose microspores were completely aborted with severely absent exine, and tapetums were abnormally developed. Genetic analyses indicated that the three male-sterile mutants belonged to allelic mutation and were triggered by the same recessive nuclear gene. MutMap-based gene mapping and kompetitive allele-specific PCR (KASP) analysis demonstrated that three different single-nucleotide polymorphisms (SNPs) of BraA09g012710.3C were responsible for the male sterility of msm1-1/2/3, respectively. BraA09g012710.3C is orthologous of Arabidopsis thaliana ACOS5 (AT1G62940), encoding an acyl-CoA synthetase in sporopollenin biosynthesis, and specifically expressed in anther, so we named BraA09g012710.3C as BrACOS5. BrACOS5 localizes to the endoplasmic reticulum (ER). Mutations of BrACOS5 resulted in decreased enzyme activities and altered fatty acid contents in msm1 anthers. As well as the transcript accumulations of putative orthologs involved in sporopollenin biosynthesis were significantly down-regulated excluding BrPKSA. These results provide strong evidence for the integral role of BrACOS5 in conserved sporopollenin biosynthesis pathway and also contribute to uncovering exine development pattern and underlying male sterility mechanism in Chinese cabbage.

Development of the maize 5.5K loci panel for genomic prediction through genotyping by target sequencing

Genotyping platforms are important for genetic research and molecular breeding. In this study, a low-density genotyping platform containing 5.5K SNP markers was successfully developed in maize using genotyping by target sequencing (GBTS) technology with capture-in-solution. Two maize populations (Pop1 and Pop2) were used to validate the GBTS panel for genetic and molecular breeding studies. Pop1 comprised 942 hybrids derived from 250 inbred lines and four testers, and Pop2 contained 540 hybrids which were generated from 123 new-developed inbred lines and eight testers. The genetic analyses showed that the average polymorphic information content and genetic diversity values ranged from 0.27 to 0.38 in both populations using all filtered genotyping data. The mean missing rate was 1.23% across populations. The Structure and UPGMA tree analyses revealed similar genetic divergences (76-89%) in both populations. Genomic prediction analyses showed that the prediction accuracy of reproducing kernel Hilbert space (RKHS) was slightly lower than that of genomic best linear unbiased prediction (GBLUP) and three Bayesian methods for general combining ability of grain yield per plant and three yield-related traits in both populations, whereas RKHS with additive effects showed superior advantages over the other four methods in Pop1. In Pop1, the GBLUP and three Bayesian methods with additive-dominance model improved the prediction accuracies by 4.89-134.52% for the four traits in comparison to the additive model. In Pop2, the inclusion of dominance did not improve the accuracy in most cases. In general, low accuracies (0.33-0.43) were achieved for general combing ability of the four traits in Pop1, whereas moderate-to-high accuracies (0.52-0.65) were observed in Pop2. For hybrid performance prediction, the accuracies were moderate to high (0.51-0.75) for the four traits in both populations using the additive-dominance model. This study suggests a reliable genotyping platform that can be implemented in genomic selection-assisted breeding to accelerate maize new cultivar development and improvement.

Construction of an SNP fingerprinting database and population genetic analysis of 329 cauliflower cultivars

Cauliflower is one of the most important vegetable crops grown worldwide. However, the lack of genetic diversity information and efficient molecular markers hinders efforts to improve cauliflower. This study aims to construct DNA fingerprints for 329 cauliflower cultivars based on SNP markers and the KASP system. After rigorous filtering, a total of 1662 candidate SNPs were obtained from nearly 17.9 million SNP loci. The mean values of PIC, MAF, heterozygosity and gene diversity of these SNPs were 0.389, 0.419, 0.075, and 0.506, respectively. We developed a program for in silico simulations on 153 core germplasm samples to generate ideal SNP marker sets from the candidates. Finally, 41 highly polymorphic KASP markers were selected and applied to identify 329 cauliflower cultivars, mainly collected from the public market. Furthermore, based on the KASP genotyping data, we performed phylogenetic analysis and population structure analysis of the 329 cultivars. As a result, these cultivars could be classified into three major clusters, and the classification patterns were significantly related to their curd solidity and geographical origin. Finally, fingerprints of the 329 cultivars and 2D barcodes with the genetic information of each sample were generated. The fingerprinting database developed in this study provides a practical tool for identifying the authenticity and purity of cauliflower seeds and valuable genetic information about the current cauliflower cultivars.

Targeted Identification of Rice Grain-Associated Gene Allelic Variation Through Mutation Induction, Targeted Sequencing, and Whole Genome Sequencing Combined with a Mixed-Samples Strategy

BACKGROUND

The mining of new allelic variation and the induction of new genetic variability are the basis for improving breeding efficiency.

RESULTS

In this study, in total, 3872 heavy ion-irradiated M₂ generation rice seeds and individual leaves were collected. The grain length was between 8 and 10.22 mm. The grain width was between 1.54 and 2.87 mm. The results showed that there was extensive variation in granulotype. The allelic variation in GS3 and GW5 was detected in 484 mixed samples (8:1) using targeted sequencing technology, and 12 mixed samples containing potential mutations and 15 SNPs were obtained; combined with Sanger sequencing and phenotype data, 13 key mutants and their corresponding SNPs were obtained; protein structural and functional analysis of key mutants screened out 6 allelic variants leading to altered grain shape, as well as the corresponding mutants, including long-grain mutants GS3-2 and GS3-7, short-grain mutants GS3-3 and GS3-5, wide-grain mutant GW5-1 and narrow-grain mutant GW5-4; whole genome sequencing identified new grain length gene allelic variants GS3-G1, GS3-G2 and GS3-G3.

CONCLUSION

Based on the above studies, we found 6 granulotype mutants and 9 granulotype-related allelic variants, which provided new functional gene loci and a material basis for molecular breeding and genotype mutation and phenotype analysis. We propose a method for targeted identification of allelic variation in rice grain type genes by combining targeted sequencing of mixed samples and whole genome sequencing. The method has the characteristics of low detection cost, short detection period, and flexible detection of traits and genes.

Selection and Validation of 48 KASP Markers for Variety Identification and Breeding Guidance in Conventional and Hybrid Rice (Oryza sativa L.)

BACKGROUND

Breeding of conventional and hybrid rice (Oryza sativa L.) have solved hunger problems and increased farmers' income in the world. Molecular markers have been widely used in marker-assisted breeding and identification of larger numbers of different bred varieties in the past decades. The recently developed SNP markers are applied for more stable and detectable compared with other markers. But the cost of genotyping lots SNPs is high. So, it is essential to select less representative SNPs and inexpensive detecting methods to lower the cost and accelerate variety identification and breeding process. KASP (Kompetitive Allele-Specific PCR) is a flexible method to detect the SNPs, and large number of KASP markers have been widely used in variety identification and breeding. However, the ability of less KASP markers on massive variety identification and breeding remains unknown.

RESULTS

Here, 48 KASP markers were selected from 378 markers to classify and analyze 518 varieties including conventional and hybrid rice. Through analyzing the population structure, the 48 markers could almost represent the 378 markers. In terms of variety identification, the 48 KASP markers had a 100% discrimination rate in 53 conventional indica varieties and 193 hybrid varieties, while they could distinguish 89.1% conventional japonica rice from different breeding institutes. Two more markers added would increase the ratio from 68.38 to 77.94%. Additionally, the 48 markers could be used for classification of subpopulations in the bred variety. Also, 8 markers had almost completely different genotypes between japonica and indica, and 3 markers were found to be very important for japonica hybrid rice. In hybrid varieties, the heterozygosity of chromosomes 3, 6 and 11 was relatively higher than others.

CONCLUSIONS

Our results showed that 48 KASP markers could be used to identify rice varieties, and the panel we tested could provide a database for breeders to identify new breeding lines. Also, the specific markers we found were useful for marker-assisted breeding in rice, including conventional and hybrid.

Advances in Genetics and Molecular Breeding of Broccoli

Broccoli (Brassica oleracea L. var. italica) is one of the most important vegetable crops cultivated worldwide. The market demand for broccoli is still increasing due to its richness in vitamins, anthocyanins, mineral substances, fiber, secondary metabolites and other nutrients. The famous secondary metabolites, glucosinolates, sulforaphane and selenium have protective effects against cancer. Significant progress has been made in fine-mapping and cloning genes that are responsible for important traits; this progress provides a foundation for marker-assisted selection (MAS) in broccoli breeding. Genetic engineering by the well-developed Agrobacterium tumefaciens-mediated transformation in broccoli has contributed to the improvement of quality; postharvest life; glucosinolate and sulforaphane content; and resistance to insects, pathogens and abiotic stresses. Here, we review recent progress in the genetics and molecular breeding of broccoli. Future perspectives for improving broccoli are also briefly discussed.