An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)

KASP-IEva: an intelligent typing evaluation model for KASP primers

KASP marker technology has been used in molecular marker-assisted breeding because of its high efficiency and flexibility, and an intelligent evaluation model of KASP marker primer typing results is essential to improve the efficiency of marker development on a large scale. To this end, this paper proposes a gene population delineation method based on NTC identification module and data distribution judgment module to improve the accuracy of K-Means clustering, and introduces a decision tree to construct the KASP-IEva primer typing evaluation model. The model firstly designs the NTC identification module and data distribution judgment module to extract four types of data, grouping and categorizing to achieve the improvement of the distinguishability of amplification product signals; secondly, the K-Means algorithm is used to aggregate and classify the data, to visualize the five aggregated clusters and to obtain the morphology location eigenvalues; lastly, the evaluation criteria for the typing effect level are constructed, and the logical decision tree is used to make conditional discrimination on the eigenvalues in order to realize the score prediction. The performance of the model was tested by the KASP marker typing test results of 2519 groups of cotton varieties, and the following conclusions were obtained: the model is able to visualize the aggregation and classification effects of the amplification products of NTC, pure genotypes, heterozygous genotypes, and untyped genotypes, enabling rapid and accurate KASP marker typing evaluation. Comparing and analyzing the model evaluation results with the expert evaluation results, the average accuracy rate of the four grades evaluated by the model was 87%, and the overall evaluation results showed an uneven distribution of the grades with significant differential characteristics. When evaluating 2519 KASP fractal maps, the expert evaluation consumes 15 hours, and the model evaluation only uses 8min27.45s, which makes the model intelligent evaluation significantly better than the expert evaluation from the perspective of time. The establishment of the model will further enhance the application of KASP markers in molecular marker-assisted breeding and provide technical support for the large-scale screening and identification of excellent genotypes.

BrWAX3, Encoding a β-ketoacyl-CoA Synthase, Plays an Essential Role in Cuticular Wax Biosynthesis in Chinese Cabbage

In this study, we identified a novel glossy mutant from Chinese cabbage, named SD369, and all wax monomers longer than 26 carbons were significantly decreased. Inheritance analysis revealed that the glossy trait of SD369 was controlled by a single recessive locus, BrWAX3. We fine-mapped the BrWAX3 locus to an interval of 161.82 kb on chromosome A09. According to the annotated genome of Brassica rapa, Bra024749 (BrCER60.A09), encoding a β-ketoacyl-CoA synthase, was identified as the candidate gene. Expression analysis showed that BrCER60.A09 was significantly downregulated in all aerial organs of glossy plants. Subcellular localization indicated that the BrCER60.A09 protein functions in the endoplasmic reticulum. A 5567-bp insertion was identified in exon 1 of BrCER60.A09 in SD369, which lead to a premature stop codon, thus causing a loss of function of the BrCER60.A09 enzyme. Moreover, comparative transcriptome analysis revealed that the ‘cutin, suberine, and wax biosynthesis’ pathway was significantly enriched, and genes involved in this pathway were almost upregulated in glossy plants. Further, two functional markers, BrWAX3-InDel and BrWAX3-KASP1, were developed and validated. Overall, these results provide a new information for the cuticular wax biosynthesis and provide applicable markers for marker-assisted selection (MAS)-based breeding of Brassica rapa.

Development of SLAF-Sequence and Multiplex SNaPshot Panels for Population Genetic Diversity Analysis and Construction of DNA Fingerprints for Sugarcane

A genetic diversity analysis and identification of plant germplasms and varieties are important and necessary for plant breeding. Deoxyribonucleotide (DNA) fingerprints based on genomic molecular markers play an important role in accurate germplasm identification. In this study, Specific-Locus Amplified Fragment Sequencing (SLAF-seq) was conducted for a sugarcane population with 103 cultivated and wild accessions. In total, 105,325 genomic single nucleotide polymorphisms (SNPs) were called successfully to analyze population components and genetic diversity. The genetic diversity of the population was complex and clustered into two major subpopulations. A principal component analysis (PCA) showed that these accessions could not be completely classified based on geographical origin. After filtration, screening, and comparison, 192 uniformly-distributed SNP loci were selected for the 32 chromosomes of sugarcane. An SNP complex genotyping detection system was established using the SNaPshot typing method and used for the precise genotyping and identification of 180 sugarcane germplasm samples. According to the stability and polymorphism of the SNPs, 32 high-quality SNP markers were obtained and successfully used to construct the first SNP fingerprinting and quick response codes (QR codes) for sugarcane. The results provide new insights for genotyping, classifying, and identifying germplasm and resources for sugarcane breeding

Agogbua J, R. Keyagha E, I. Nkanga I. Carotenoids in Cassava (Manihot esculenta Crantz)

Cassava is produced globally and consumed as an important staple in Africa for its calories, but the crop is deficient in micronutrients such as vitamin A. Pro-vitamin A carotenoids including β-carotene are precursors of vitamin A in the human body. Carotenoids are generally associated with colors of fruits and vegetables. Although most cassava varieties have white tuberous roots and generally accepted, naturally; some cassava roots are colored yellow and contain negligible amounts of vitamin A. Several genes have been identified in the carotenoids biosynthesis pathway of plants, but studies show that Phytoene synthase 2 (PSY2), lycopene epsilon cyclase, and β-carotene hydroxylase genes have higher expression levels in yellow cassava roots. So far, the PSY2 gene has been identified as the key gene associated with carotenoids in cassava. Some initiatives are implementing conventional breeding to increase pro-vitamin A carotenoids in cassava roots, and much success has been achieved in this regard. This chapter highlights various prediction tools employed for carotenoid content in fresh cassava roots, including molecular marker-assisted strategies developed to fast-track the conventional breeding for increased carotenoids in cassava.

Two fingerprinting sets for Humulus lupulus based on KASP and microsatellite markers

Verification of clonal identity of hop (Humulus lupulus L.) cultivars within breeding programs and germplasm collections is vital to conserving genetic resources. Accurate and economic DNA-based tools are needed in dioecious hop to confirm identity and parentage, neither of which can be reliably determined from morphological observations. In this study, we developed two fingerprinting sets for hop: a 9-SSR fingerprinting set containing high-core repeats that can be run in a single PCR reaction and a kompetitive allele specific PCR (KASP) assay of 25 single nucleotide polymorphisms (SNPs). The SSR set contains a sex-linked primer pair, HI-AGA7, that was used to genotype 629 hop accessions from the US Department of Agriculture (USDA) National Clonal Germplasm Repository (NCGR), the USDA Forage Seed and Cereal Research (FSCR), and the University of Nebraska-Lincoln (UNL) collections. The SSR set identified unique genotypes except for 89 sets of synonymous samples. These synonyms included: cultivars with different designations, the same cultivars from different sources, heat-treated clones, and clonal variants. Population structure analysis clustered accessions into wild North American (WNA) and cultivated groups. Diversity was slightly higher in the cultivated samples due to larger sample size. Parentage and sib-ship analyses were used to identify true-to-type cultivars. The HI-AGA7 marker generated two male- and nine female-specific alleles among the cultivated and WNA samples. The SSR and KASP fingerprinting sets were compared in 190 samples consisting of cultivated and WNA accession for their ability to confirm identity and assess diversity and population structure. The SSR fingerprinting set distinguished cultivars, selections and WNA accessions while the KASP assays were unable to distinguish the WNA samples and had lower diversity estimates than the SSR set. Both fingerprinting sets are valuable tools for identity confirmation and parentage analysis in hop for different purposes. The 9-SSR assay is cost efficient when genotyping a small number of wild and cultivated hop samples (<96) while the KASP assay is easy to interpret and cost efficient for genotyping a large number of cultivated samples (multiples of 96).

Map-Based Cloning and Characterization of Br-dyp1, a Gene Conferring Dark Yellow Petal Color Trait in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Flower color is an important trait in Brassica species. However, genes responsible for the dark yellow flower trait in Chinese cabbage have not been reported. In this study, we identified a dark-yellow-flowered Chinese cabbage line SD369. Genetic analysis indicated that the dark yellow flower trait in SD369 was controlled by a single recessive locus, Br-dyp1 (dark yellow petal color 1 in Brassica rapa). Using bulked segregant RNA sequencing and kompetitive allele-specific PCR assays, Br-dyp1 was fine-mapped to an interval of 53.6 kb on chromosome A09. Functional annotation analysis, expression analysis, and sequence variation analysis revealed that Bra037130 (BraA09.ZEP), which encodes a zeaxanthin epoxidase, was the most likely candidate gene for Br-dyp1. Carotenoid profile analysis suggested that Bra037130 (BraA09.ZEP) might participate in the epoxidation from zeaxanthin to violaxanthin. The 679 bp insertion in dark yellow petal caused premature stop codon, thus caused the loss-of-function of the enzyme zeaxanthin epoxidase (ZEP), which disturbed the carotenoid metabolism, and caused the increased accumulation of total carotenoid, and finally converted the flower color from yellow to dark yellow. Comparative transcriptome analysis also showed that the "carotenoid biosynthesis" pathway was significantly enriched, and genes involved in carotenoid degradation and abscisic acid biosynthesis and metabolism were significantly downregulated. Furthermore, we developed and validated the functional marker Br-dyp1-InDel for Br-dyp1. Overall, these results provide insight into the molecular basis of carotenoid-based flower coloration in B. rapa and reveal valuable information for marker-assisted selection breeding in Chinese cabbage.

BrWAX2 plays an essential role in cuticular wax biosynthesis in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

Map-based cloning was used to identify the BrWAX2 gene, which was involved in the cuticular wax biosynthesis. The malfunction of BrWAX2 together with other reduced expression of genes in alkane-forming pathway caused the glossy phenotype. Cuticular wax covering the outer plant surface plays various roles in protecting against biotic and abiotic stresses. Wax-less mutant shows glossy in stem and leaf surface and plays important roles in enriching Chinese cabbage germplasm resources for breeding brilliant green varieties. However, genes responsible for the glossy trait in Chinese cabbage are rarely reported. In this study, we identified a glossy Chinese cabbage line Y1211-1. Genetic analysis indicated that the glossy trait in Y1211-1 was controlled by a single recessive locus, BrWAX2 (Brassica rapa WAX 2). Using bulked segregant sequencing (BSA-Seq) and kompetitive allele-specific PCR (KASP) assays, BrWAX2 was fine-mapped to an interval of 100.78 kb. Functional annotation analysis, expression analysis, and sequence variation analysis revealed that Bra032670, homologous to CER1 in Arabidopsis, was the most likely candidate gene for BrWAX2. The gene Bra032670 was absent in glossy mutant. Cuticular wax composition analysis and RNA-Seq analysis suggested that the absence of BrWAX2 together with the decreased expression of other genes in alkane-forming pathway reduced the wax amount and caused the glossy phenotype. Furthermore, we developed and validated the functional marker BrWAX2-sp for BrWAX2. Overall, these results provide insight into the molecular mechanism underlying cuticular wax biosynthesis and reveal valuable information for marker-assisted selection (MAS) breeding in Chinese cabbage.

Genetic Mapping and Identification of the Candidate Genes for Mottled Rind in Cucumis melo L

The rind appearance of melon is one of the most vital commercial quality traits which determines the preferences and behavior of consumers toward the consumption of melon. In this study, we constructed an F₂ population derived from SC (mottled rind) and MG (non-mottled rind) lines for mapping the mottled rind gene(s) in melon. Genetic analysis showed that there were two dominant genes (CmMt1 and CmMt2) with evidence of epistasis controlling the mottled rind. Meanwhile, the phenotypic segregation ratio implied that the immature rind color had an epistatic effect on the mottled rind, which was regulated by CmAPRR2. A Kompetitive Allele-Specific PCR (KASP) DNA marker (CmAPRR2 ^SNP(G/T) ) was developed and shown to co-segregate with rind color, confirming that CmAPRR2 was CmMt1. Using bulked segregant analysis sequencing and KASP assays, CmMt2 was fine-mapped to an interval of 40.6 kb with six predicted genes. Functional annotation, expression analysis, and sequence variation analyses confirmed that AtCPSFL1 homolog, MELO3C026282, was the most likely candidate gene for CmMt2. Moreover, pigment content measurement and transmission electron microscopy analysis demonstrated that CmMt2 might participate in the development of chloroplast, which, in turn, decreases the accumulation of chlorophyll. These results provide insight into the molecular mechanism underlying rind appearance and reveal valuable information for marker-assisted selection breeding in melon.

Fine Mapping and Candidate Gene Identification of a White Flower Gene BrWF3 in Chinese Cabbage (Brassica rapa L. ssp. pekinensis)

Flower color is an important trait in plants. However, genes responsible for the white flower trait in Chinese cabbage are rarely reported. In this study, we constructed an F₂ population derived from the Y640-288 (white flower) and Y641-87 (yellow flower) lines for the fine mapping of the white flower gene BrWF3 in Chinese cabbage. Genetic analysis indicated that BrWF3 was controlled by a single recessive gene. Using BSA-seq and KASP assays, BrWF3 was fine-mapped to an interval of 105.6 kb. Functional annotation, expression profiling, and sequence variation analyses confirmed that the AtPES2 homolog, Bra032957, was the most likely candidate gene for BrWF3. Carotenoid profiles and transmission electron microscopy analysis suggested that BrWF3 might participate in the production of xanthophyll esters (particularly violaxanthin esters), which in turn disrupt chromoplast development and the formation of plastoglobules (PGs). A SNP deletion in the third exon of BrWF3 caused the loss of protein function, and interfered with the normal assembly of PGs, which was associated with reduced expression levels of genes involved in carotenoid metabolism. Furthermore, we developed and validated the functional marker TXBH83 for BrWF3. Our results provide insight into the molecular mechanism underlying flower color pigmentation and reveal valuable information for marker-assisted selection (MAS) breeding in Chinese cabbage.