Gene-flow investigation between garden and wild roses planted in close distance

Rose is a major ornamental plant, and a lot of cultivars with attractive morphology, color and scent have been generated by classical breeding. Recent progress of genetic modification produces a novel cultivar with attractive features. In both cases, a major problem is the gene-flow from cultivated or genetically modified (GM) plants to wild species, causing reduction of natural population. To investigate whether gene-flow occurs in wild species, molecular analysis with DNA markers with higher efficient technique is useful. Here we investigated the gene-flow from cultivated roses (Rosa×hybrida) to wild rose species planted in close distance in the field. The overlapping flowering periods and visiting insects suggest that pollens were transported by insects between wild and cultivated roses. We examined the germination ratio of seeds from wild species, and extracted DNA and checked with KSN and APETALA2 (AP2) DNA markers to detect transposon insertions. Using two markers, we successfully detected the outcross between wild and cultivated roses. For higher efficiency, we established a bulking method, where DNA, leaves or embryos were pooled, enabling us to that check the outcross of many plants. Our results suggest that wild species and garden cultivars can cross in close distance, so that they should be planted in distance, and checked the outcross with multiple DNA markers.

Identification of QTLs and allelic effect controlling lignan content in sesame (Sesamum indicum L.) using QTL-seq approach

Sesame (Sesamum indicum L.), an oilseed crop, is gaining worldwide recognition for its healthy functional ingredients as consumption increases. The content of lignans, known for their antioxidant and anti-inflammatory effects, is a key agronomic trait that determines the industrialization of sesame. However, the study of the genetics and physiology of lignans in sesame is challenging, as they are influenced by multiple genes and environmental factors, therefore, the understanding of gene function and synthetic pathways related to lignan in sesame is still limited. To address these knowledge gaps, we conducted genetic analyses using F7 recombinant inbred line (RIL) populations derived from Goenbaek and Gomazou as low and high lignin content variants, respectively. Using the QTL-seq approach, we identified three loci, qLignan1-1, qLignan6-1, and qLignan11-1, that control lignan content, specifically sesamin and sesamolin. The allelic effect between loci was evaluated using the RIL population. qLignan6-1 had an additive effect that increased lignan content when combined with the other two loci, suggesting that it could be an important factor in gene pyramiding for the development of high-lignan varieties. This study not only highlights the value of sesame lignan, but also provides valuable insights for the development of high-lignan varieties through the use of DNA markers in breeding strategies. Overall, this research contributes to our understanding of the importance of sesame oil and facilitates progress in sesame breeding for improved lignan content.

Development of real-time PCR-based markers for differentiation of Oplopanax elatus and Aralia cordata in commercial food products

Oplopanax elatus and Aralia cordata, commonly referred to as "Dureub" in Korea, are generally used as medicinal or food raw materials. Although O. elatus, a rare and endangered plant, is typically sold at high prices, the more abundant A. cordata is comparatively inexpensive. Given their common names and morphological root similarities, both plants can easily be confused, thereby providing potential opportunities for fraudulent use in food products. Species-specific molecular markers that can be used for quantitative real-time PCR (qPCR) analysis were developed. Verification of the six primer pairs revealed a correlation coefficient greater than 0.99, with a slope between -3.33 and -3.56. The assay confirmed specificity based on an analysis of 14 non-target plant species and verified its practicality using 10 commercial products with reliability based on a blind test. Thus, qPCR assays can contribute to food safety and protect consumer rights and interests.

Supplementary Information

The online version of this article contains supplementary material available 10.1007/s10068-023-01313-1.

A potent allele marker related to low bull conception rate in Japanese Black bulls

Over the years, there has been considerable variation in the bull conception rate (BCR) of Japanese Black cattle; moreover, several Japanese Black bulls with a low BCR of ≤10% have been identified. However, the alleles responsible for the low BCR are not determined yet. Therefore, in this study, we aimed to identify single-nucleotide polymorphisms (SNPs) for predicting low BCR. To this end, the genome of Japanese Black bulls was comprehensively examined by a genome-wide association study with whole-exome sequencing (WES), and the effect of the identified marker regions on BCR was determined. The WES analysis of six sub-fertile bulls with a BCR of ≤10% and 73 normal bulls with a BCR of ≥40% identified a homozygous genotype for low BCR in Bos taurus autosome 5 in the region between 116.2 and 117.9 Mb. The g.116408653G > A SNP in this region had the most significant effect on the BCR (P-value = 1.0 × 10^-23), and the GG (55.4 ± 11.2%) and AG (54.4 ± 9.4%) genotypes in the SNP had a higher phenotype than the AA (9.5 ± 6.1%) genotype for the BCR. The mixed model analysis revealed that g.116408653G > A was related to approximately 43% of the total genetic variance. In conclusion, the AA genotype of g.116408653G > A is a useful index for identifying sub-fertile Japanese Black bulls. Some positive and negative effects of SNP on the BCR were presumed to identify the causative mutations, which can help evaluate bull fertility.

Establishing DNA markers to differentiate Agastache rugosa and Pogostemon cablin, which are confusedly used as medicinal herbs, using real-time PCR

Agastache rugosa and Pogostemon cablin are used as medicinal herbs and aromatic plants and belong to the family Lamiaceae. Despite differences in composition and physicochemical properties, both plants are frequently sold as the medical substance "Kwakhyang" in some Asian countries. Molecular markers were established to distinguish between the two plants using quantitative real-time PCR. Species-specific primers were designed in the nuclear internal transcribed spacer region of ribosomal DNA and in the chloroplast genes matK, rbcL, and rpoB. Six primer sets were tested, the correlation coefficient was higher than 0.99, and the slope was approximately - 3.36 to - 3.58. Efficiency ranged from 90.13 to 98.52%. The developed real-time PCR assay was validated with 14 off-target species, and its reliability was verified through blind testing of 14 commercial products. The assay developed here may help protect consumer rights, and the designed primers can be used to distinguish between the target species.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01176-y.

Deoxyribonucleic Acid Barcoding for the Identification of Botanicals

The Natural Herbal Products industry uses botanicals or herbs as raw materials for production of herbal products or dietary supplements. Recently, the demand for natural herbal products has increased tremendously and this has led to adulteration and to counterfeit herbal products. The present chapter deals with currently used molecular methods from "simple" single genomic regions to high-throughput whole genome or transcriptome sequencing methods used in the identification of botanicals.

Polymorphisms in Pattern Recognition Receptor Genes Are Associated with Respiratory Disease Severity in Pig Farms

Reduced productivity caused by infections, particularly respiratory diseases, is a serious problem in pig farming. We have previously reported polymorphisms in porcine pattern recognition receptor genes affecting molecular functions and demonstrated that the 2197A/C polymorphism in the nucleotide-binding oligomerization domain containing 2 (NOD2) gene influences porcine circovirus 2-induced mortality. Here, we investigated how these polymorphisms affect respiratory disease-induced lesions, using samples from a slaughterhouse dealing with pigs from two farms. Lung lesions were evaluated using two scoring systems, Goodwin (GW) and slaughterhouse pleuritis evaluation system (SPES), to determine the influence of Mycoplasma hyopneumoniae (Mhp) and Actinobacillus pleuropneumoniae (App), respectively. SPES scores were significantly higher when the 1205T allele of Toll-like receptor 5 (TLR5-1205T), rather than TLR5-1205C, was present. On the farm with more severe Mhp invasion, lower GW lesion scores were significantly associated with the presence of the NOD-like receptor family pyrin domain containing 3 (NLRP3)-2906G allele; where App invasion was worse, lower SPES scores were significantly associated with the presence of the NOD2-2197C allele. Combinations of polymorphisms in pattern recognition receptor genes can therefore be utilized for breeding for resistance against respiratory diseases in pigs. DNA markers of these polymorphisms can thus be used to improve productivity by reducing respiratory diseases due to bacterial pathogens in pig livestock.

PMEL p.Leu18del dilutes coat color of Kumamoto sub-breed of Japanese Brown cattle

Background

Coat color is important for registration and maintenance of livestock. Standard coat color of Kumamoto sub-breed of Japanese Brown cattle is solid brown, but individuals with diluted coat color have been observed recently. In this study, we attempted to identify polymorphism(s) responsible for coat color dilution by whole genome analysis.

Results

One of the diluted cattle possessed 7302 exonic polymorphisms which could affect genes’ function. Among them, 14 polymorphisms in 10 coat color-related genes were assumed to be specific for the diluted cattle. Subsequent genotyping with three diluted cattle and 74 standard cattle elucidated that PMEL p.Leu18del was the causative polymorphism for coat color dilution in this sub-breed. Individuals with del/del type of this polymorphism showed diluted coat color, but coat color of heterozygotes were intermediate with various dilution rates.

Conclusions

Coat color dilution of Kumamoto sub-breed was caused by PMEL p.Leu18del. The causative del allele has been detected in several genetically distant cattle breeds, suggesting that PMEL p.Leu18del can be used as a DNA marker to control cattle coat color.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08916-8.

Identification of Candidate Genes Responsible for Flower Colour Intensity in Gentiana triflora

Gentians cultivated in Japan (Gentiana triflora and Gentiana scabra and hybrids) have blue flowers, but flower colour intensity differs among cultivars. The molecular mechanism underlying the variation in flower colour intensity is unclear. Here, we produced F₂ progeny derived from an F₁ cross of intense- and faint-blue lines and attempted to identify the genes responsible for flower colour intensity using RNA-sequencing analyses. Comparative analysis of flower colour intensity and transcriptome data revealed differentially expressed genes (DEGs), although known flavonoid biosynthesis-related genes showed similar expression patterns. From quantitative RT-PCR (qRT-PCR) analysis, we identified two and four genes with significantly different expression levels in the intense- and faint-blue flower lines, respectively. We conducted further analyses on one of the DEGs, termed GtMIF1, which encodes a putative mini zinc-finger protein homolog, which was most differently expressed in faint-blue individuals. Functional analysis of GtMIF1 was performed by producing stable tobacco transformants. GtMIF1-overexpressing tobacco plants showed reduced flower colour intensity compared with untransformed control plants. DNA-marker analysis also confirmed that the GtMIF1 allele of the faint-blue flower line correlated well with faint flower colour in F₂ progeny. These results suggest that GtMIF1 is one of the key genes involved in determining the flower colour intensity of gentian.

QTL-Seq Analysis for Identification of Resistance Loci to Bacterial Canker in Tomato

Bacterial canker caused by Clavibacter michiganensis (Cm) is one of the most economically important vascular diseases causing unilateral leaf wilting, stem canker, a bird's-eye lesion on fruit, and whole plant wilting in tomato. There is no commercially available cultivar with bacterial canker resistance, and genomics-assisted breeding can accelerate the development of cultivars with enhanced resistance. Solanum lycopersicum "Hawaii 7998" was found to show bacterial canker resistance. A Quantitative trait loci (QTL)-seq was performed to identify the resistance loci using 909 F₂ individuals derived from a cross between S. lycopersicum "E6203" (susceptible) and "Hawaii 7998," and a genomic region (37.24-41.15 Mb) associated with bacterial canker resistance on chromosome 6 (Rcm6) was found. To dissect the Rcm6 region, 12 markers were developed and several markers were associated with the resistance phenotypes. Among the markers, the Rcm6-9 genotype completely matched with the phenotype in the 47 cultivars. To further validate the Rcm6 as a resistance locus and the Rcm6-9 efficiency, subsequent analysis using F₂ and F₃ progenies was conducted. The progeny individuals with homozygous resistance allele at the Rcm6-9 showed significantly lower disease severity than those possessing homozygous susceptibility alleles. Genomes of five susceptible and two resistant cultivars were analyzed and previously known R-genes were selected to find candidate genes for Rcm6. Nucleotide-binding leucine-rich repeat, receptor-like kinase, and receptor-like protein were identified to have putative functional mutations and show differential expression upon the Cm infection. The DNA markers and candidate genes will facilitate marker-assisted breeding and provide genetic insight of bacterial canker resistance in tomato.

Development of DNA markers for improvement of meat quality in a Japanese Black cattle population in Hyogo Prefecture

The polymorphisms associated with economic traits in livestock animals provide useful information as genetic indicators for breeding improvement. Over the last two decades, several DNA markers have been developed in Japanese Black cattle; however, the effect of these markers differs across populations due to differences in their genetic structures and backgrounds. As such, there is a need to verify the effectiveness of these markers in each population. This review summarizes the effectiveness of previously reported markers on carcass traits and the development of novel DNA markers in a Japanese Black cattle population in Hyogo Prefecture. As result of genome wide association studies and resequencing analyses, two novel significant markers associated with meat quality-related traits (beef marbling and fatty acid composition) were developed. These findings will lead to the identification of responsible genes and polymorphisms and contribute to the development of novel DNA markers for numerous traits in various cattle populations.

Parentage analysis of tea cultivars in Japan based on simple sequence repeat markers

Tea cultivars have been bred by individual selection of landraces and by crossbreeding, but the validation of the parentage is limited. In this study, we performed parentage analysis of 79 tea cultivars in Japan based on SSR markers to confirm or identify the parent-offspring relationships among them. The effectiveness of nine SSR markers for parentage analysis was validated by comparing them to the existing cleaved amplified polymorphic sequence markers. The former markers were detectable more alleles than the latter. Simulation of parentage analysis of the tea cultivars predicted biparental origins for 12 cultivars ('Houshun', 'Mie ryokuhou no. 1', 'Surugawase', 'Tenmyo', 'Yamanoibuki', 'Harumidori', 'Koushun', 'Minekaori', 'Okumusashi', 'Saemidori', 'Sofu', and 'Toyoka'), in the first five of which candidate parents of yet-to-be-defined pedigree were newly identified. Comparisons of a total of 41 SSR genotypes confirmed the newly-identified parentages of 'Asahi' for 'Tenmyo', 'Rokurou' for 'Houshun', 'Surugawase', and 'Yamanoibuki', and 'Yamatomidori' for 'Mie ryokuhou no. 1'. The maternity of seven cultivars out of the 12 was also confirmed with chloroplast DNA sequences. Uniparental origins were confirmed for 25 cultivars. This parentage analysis has improved our knowledge of tea pedigrees and will aid in the development of new cultivars.

Polyploid QTL-seq towards rapid development of tightly linked DNA markers for potato and sweetpotato breeding through whole-genome resequencing

Potato (Solanum tuberosum L.) and sweetpotato (Ipomoea batatas L.), which are nutritionally and commercially important tuberous crops, possess a perplexing heredity because of their autopolyploid genomes. To reduce cross-breeding efforts for selecting superior cultivars from progenies with innumerable combinations of traits, DNA markers tightly linked to agronomical traits are required. To develop DNA markers, we developed a method for quantitative trait loci (QTL) mapping using whole-genome next-generation sequencing (NGS) in autopolyploid crops. To apply the NGS-based bulked segregant method, QTL-seq was modified. (1) Single parent-specific simplex (unique for one homologous chromosome) single-nucleotide polymorphisms (SNPs), which present a simple segregation ratio in the progenies, were exploited by filtering SNPs by SNP index (allele frequency). (2) Clusters of SNPs, which were inherited unevenly between bulked progenies with opposite phenotypes, especially those with an SNP index of 0 for the bulk that did not display the phenotypes of interest, were explored. These modifications allowed for separate tracking of alleles located on each of the multiple homologous chromosomes. By applying this method, clusters of SNPs linked to the potato cyst nematode resistance H1 gene and storage root anthocyanin (AN) content were identified in tetraploid potato and hexaploid sweetpotato, respectively, and completely linked DNA markers were developed at the site of the presented SNPs. Thus, polyploid QTL-seq is a versatile method that is free from specialized manipulation for sequencing and construction of elaborate linkage maps and facilitates rapid development of tightly linked DNA markers in autopolyploid crops, such as potato and sweetpotato.

Comparative Transcriptome Analysis to Identify Candidate Genes for FaRCg1 Conferring Resistance Against Colletotrichum gloeosporioides in Cultivated Strawberry (Fragaria × ananassa)

Colletotrichum crown rot (CCR) caused by Colletotrichum gloeosporioides is a serious threat to the cultivated strawberry (Fragaria × ananassa). Our previous study reported that a major locus, FaRCg1, increases resistance. However, the genomic structure of FaRCg1 and potential candidate genes associated with the resistance remained unknown. Here, we performed comparative transcriptome analyses of resistant 'Florida Elyana' and susceptible 'Strawberry Festival' after infection and identified candidate genes potentially involved in resistance. In 'Florida Elyana', 6,099 genes were differentially expressed in response to C. gloeosporioides. Gene ontology analysis showed that the most upregulated genes were functionally associated with signaling pathways of plant defense responses. Three genes in the genomic region of FaRCg1 were highly upregulated: a von Willebrand Factor A domain-containing protein, a subtilisin-like protease, and a TIFY 11A-like protein. Subgenome-specific markers developed for the candidate genes were tested with a diverse panel of 219 accessions from University of Florida and North Carolina State University breeding programs. Significant and positive associations were found between the high-resolution melting (HRM) marker genotypes and CCR phenotypes. These newly developed subgenome-specific functional markers for FaRCg1 can facilitate development of resistant varieties through marker-assisted selection.

Recent advancements in molecular marker-assisted selection and applications in plant breeding programmes

Background

DNA markers improved the productivity and accuracy of classical plant breeding by means of marker-assisted selection (MAS). The enormous number of quantitative trait loci (QTLs) mapping read for different plant species have given a plenitude of molecular marker-gene associations.

Main body of the abstract

In this review, we have discussed the positive aspects of molecular marker-assisted selection and its precise applications in plant breeding programmes. Molecular marker-assisted selection has considerably shortened the time for new crop varieties to be brought to the market. To explore the information about DNA markers, many reviews have been published in the last few decades; all these reviews were intended by plant breeders to obtain information on molecular genetics. In this review, we intended to be a synopsis of recent developments of DNA markers and their application in plant breeding programmes and devoted to early breeders with little or no knowledge about the DNA markers. The progress made in molecular plant breeding, plant genetics, genomics selection, and editing of genome contributed to the comprehensive understanding of DNA markers and provides several proofs on the genetic diversity available in crop plants and greatly complemented plant breeding devices.

Short conclusion

MAS has revolutionized the process of plant breeding with acceleration and accuracy, which is continuously empowering plant breeders around the world.

RNA-Seq-based DNA marker analysis of the genetics and molecular evolution of Triticeae species

The release of high-quality chromosome-level genome sequences of members of the Triticeae tribe has greatly facilitated genetic and genomic analyses of important crops such as wheat (Triticum aestivum) and barley (Hordeum vulgare). Due to the large diploid genome size of Triticeae plants (ca. 5 Gbp), transcript analysis is an important method for identifying genetic and genomic differences among Triticeae species. In this review, we summarize our results of RNA-Seq analyses of diploid wheat accessions belonging to the genera Aegilops and Triticum. We also describe studies of the molecular relationships among these accessions and provide insight into the evolution of common hexaploid wheat. DNA markers based on polymorphisms within species can be used to map loci of interest. Even though the genome sequence of diploid Aegilops tauschii, the D-genome donor of common wheat, has been released, the diploid barley genome continues to provide key information about the physical structures of diploid wheat genomes. We describe how a series of RNA-Seq analyses of wheat relatives has helped uncover the structural and evolutionary features of genomic and genetic systems in wild and cultivated Triticeae species.

Genome sequence of Hydrangea macrophylla and its application in analysis of the double flower phenotype

Owing to its high ornamental value, the double flower phenotype of hydrangea (Hydrangea macrophylla) is one of its most important traits. In this study, genome sequence information was obtained to explore effective DNA markers and the causative genes for double flower production in hydrangea. Single-molecule real-time sequencing data followed by a Hi-C analysis were employed. Two haplotype-phased sequences were obtained from the heterozygous genome of hydrangea. One assembly consisted of 3,779 scaffolds (2.256 Gb in length and N50 of 1.5 Mb), the other also contained 3,779 scaffolds (2.227 Gb in length, and N50 of 1.4 Mb). A total of 36,930 genes were predicted in the sequences, of which 32,205 and 32,222 were found in each haplotype. A pair of 18 pseudomolecules was constructed along with a high-density single-nucleotide polymorphism (SNP) genetic linkage map. Using the genome sequence data, and two F₂ populations, the SNPs linked to double flower loci (d_jo and d_su) were discovered. DNA markers linked to d_jo and d_su were developed, and these could distinguish the recessive double flower allele for each locus, respectively. The LEAFY gene is a very likely candidate as the causative gene for d_su, since frameshift was specifically observed in the double flower accession with d_su.

Improvement of diagnostic markers for resistance to Globodera pallida and application for selection of resistant germplasms in potato breeding

Occurrence of pale potato cyst nematode, Globodera pallida (Stone) Behrens, was first recorded in Japan in 2015. Among several control measures, cultivation of resistant potato (Solanum tuberosum L.) varieties is the most effective in cost and environmental impact. As no G. pallida-resistant varieties have yet been developed in Japan, great emphasis is being placed on screening of germplasm possessing the resistance and development of the resistant varieties. In this study, we first improved previously reported DNA markers linked to the G. pallida resistance loci (GpaIV^s _adg and Gpa5) and then used these to screen more than 1,000 germplasms to select several candidate germplasms with resistance. We performed inoculation testing on the selected candidates and identified several resistant germplasms to the Japanese G. pallida population. Furthermore, we developed a simultaneous detection method combining three DNA markers linked to G. pallida and Globodera rostochiensis (Wollenweber) Behrens resistance loci. We validated the ability of C237-I marker to select resistant allele of GpaIV^s _adg and predict the presence of resistance in a Japanese breeding population. Resistant germplasms identified in this study could potentially be used to develop G. pallida-resistant varieties. The marker evaluation methods developed in this study will contribute to the efficient development of resistant varieties.

Development of a New DNA Marker for Fusarium Yellows Resistance in Brassica rapa Vegetables

In vegetables of Brassica rapa L., Fusarium oxysporum f. sp. rapae (For) or F. oxysporum f. sp. conglutinans (Foc) cause Fusarium yellows. A resistance gene against Foc (FocBr1) has been identified, and deletion of this gene results in susceptibility (focbr1-1). In contrast, a resistance gene against For has not been identified. Inoculation tests showed that lines resistant to Foc were also resistant to For, and lines susceptible to Foc were susceptible to For. However, prediction of disease resistance by a dominant DNA marker on FocBr1 (Bra012688m) was not associated with disease resistance of For in some komatsuna lines using an inoculation test. QTL-seq using four F₂ populations derived from For susceptible and resistant lines showed one causative locus on chromosome A03, which covers FocBr1. Comparison of the amino acid sequence of FocBr1 between susceptible and resistant alleles (FocBr1 and FocBo1) showed that six amino acid differences were specific to susceptible lines. The presence and absence of FocBr1 is consistent with For resistance in F₂ populations. These results indicate that FocBr1 is essential for For resistance, and changed amino acid sequences result in susceptibility to For. This susceptible allele is termed focbr1-2, and a new DNA marker (focbr1-2m) for detection of the focbr1-2 allele was developed.

Development of PCR-based DNA marker for detection of white carrot contamination caused by Y2 locus

In carrot (Daucus carota L.), the taproot colors orange, yellow and white are determined mostly by the Y, Y2, and Or loci. One of the most severe issues in carrot seed production is contamination by wild white carrot. To evaluate the contamination ratio, easily detectable DNA markers for white carrot are desired. To develop PCR-based DNA markers for the Y2 locus, we have re-sequenced two orange-colored carrot cultivars at our company (Fujii Seed, Japan), as well as six white- and one light-orange-colored carrots that contaminated our seed products. Within the candidate region previously reported for the Y2 locus, only one DNA marker, Y2_7, clearly distinguished white carrots from orange ones in the re-sequenced samples. The Y2_7 marker was further examined in 12 of the most popular hybrid orange cultivars in Japan, as well as 'Nantes' and 'Chantenay Red Cored 2'. The Y2_7 marker showed that all of the orange cultivars examined had the orange allele except for 'Beta-441'. False white was detected in the orange-colored 'Beta-441'. The Y2_7 marker detected white root carrot contamination in an old open-pollinated Japanese cultivar, 'Nakamura Senkou Futo'. This marker would be a useful tool in a carrot seed quality control for some cultivars.

Linkage analysis of rice bacterial blight resistance gene xa20 in XM6, a mutant line from IR24

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is an important disease constraining rice (Oryza sativa L.) production worldwide. The XM6 line was induced by N-methyl-N-nitrosourea from IR24, an Indica cultivar that is susceptible to Philippine and Japanese Xoo races. XM6 was confirmed to carry a recessive gene named xa20, resistant to six Philippine and five Japanese Xoo races. The chromosomal gene location was found using 10 plants with the shortest lesion length in an F₂ population consisting of 298 plants from a susceptible Japonica variety Koshihikari × XM6. Analysis using PCR-based DNA markers covering the whole rice genome indicated the gene as located on the distal region of the long arm of chromosome 3. The IKC3 line carries IR24 genetic background with Koshihikari fragment on chromosome 3 where a resistance gene was thought to be located. The F₂ population from IKC3 × XM6 clearly showed a bimodal distribution separating resistant and susceptible plants. Further linkage analysis conducted using this F₂ population revealed that xa20 is located within the 0.8 cM region flanked by DNA markers KIC3-33.88 (33.0 Mb) and KIC3-34.06 (33.2 Mb). This study yields important findings for resistance breeding and for the genetic mechanism of Xoo resistance.

Molecular approaches for improving oil palm for oil

The oil palm, originating from Africa, is the most productive oil crop species. Palm oil is an important source of edible oil. Its current global plantation area is over 23 million ha. The theoretical oil yield potential of the oil palm is 18.2 tons/ha/year. However, current average oil yield is only 3.8 tons/ha/year. In the past 100 years, conventional breeding and improvement of field management played important roles in increasing oil yield. However, conventional breeding for trait improvement was limited by its very long (10-20 years) phenotypic selection cycle, although it improved oil yield by ~10-20% per generation. Molecular breeding using novel molecular technologies will accelerate genetic improvement and may reduce the need to deforest and to use arable land for expanding oil palm plantations, which in turn makes palm oil more sustainable. Here, we comprehensively synthesize information from relevant literature of the technologies, achievements, and challenges of molecular approaches, including tissue culture, haploid breeding, mutation breeding, marker-assisted selection (MAS), genomic selection (GS), and genome editing (GE). We propose the characteristics of ideal palms and suggest a road map to breed ideal palms for sustainable palm oil.

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

A longitudinal study on morpho-genetic diversity of pathogenic Rhizoctonia solani from sugar beet and dry beans of western Nebraska

Background

Root and stem rot caused by Rhizoctonia solani is a serious fungal disease of sugar beet and dry bean production in Nebraska. Rhizoctonia root rot and crown rot in sugar beet and dry bean have reduced the yield significantly and has also created problems in storage. The objective of this study was to analyze morpho-genetic diversity of 38 Rhizoctonia solani isolates from sugar beet and dry bean fields in western Nebraska collected over 10 years. Morphological features and ISSR-based DNA markers were used to study the morphogenetic diversity.

Results

Fungal colonies were morphologically diverse in shapes, aerial hyphae formation, colony, and sclerotia color. Marker analysis using 19 polymorphic ISSR markers showed polymorphic bands ranged from 15 to 28 with molecular weight of 100 bp to 3 kb. Polymorphic loci ranged from 43.26–92.88%. Nei genetic distance within the population ranged from 0.03–0.09 and Shannon diversity index varied from 0.24–0.28. AMOVA analysis based on ΦPT values showed 87% variation within and 13% among the population with statistical significance (p < 0.05). Majority of the isolates from sugar beet showed nearby association within the population. A significant number of isolates showed similarity with isolates of both the crops suggesting their broad pathogenicity. Isolates were grouped into three different clusters in UPGMA based cluster analysis using marker information. Interestingly, there was no geographical correlation among the isolates. Principal component analysis showed randomized distribution of isolates from the same geographical origin. Identities of the isolates were confirmed by both ITS-rDNA sequences and pathogenicity tests.

Conclusion

Identification and categorization of the pathogen will be helpful in designing integrated disease management guidelines for sugar beet and dry beans of mid western America.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12866-020-02026-9.

DNA marker development by the allele-specific detection of powdery mildew resistance loci derived from Japanese domestic tobacco cultivar 'Kokubu'

Japanese domestic tobacco (Nicotiana tabacum L.) cultivar 'Kokubu' shows high powdery mildew resistance controlled by recessive alleles at two loci, and these alleles have been widely used as a resource for powdery mildew resistance in tobacco breeding. However, the introduction of this trait by conventional breeding takes much work because of the requirement for test crosses with the parental strains and inoculation tests using active fungi to confirm the introduction of two recessive alleles during back-crossing. Recently, we found that powdery mildew resistance in 'Kokubu' is caused by splice site mutations of two MILDEW LOCUS O genes, NtMLO1 and NtMLO2. Here, we report DNA markers that detect mutations of the NtMLO1/2 genes based on the cleaved amplified polymorphic sequence (CAPS) or allele-specific polymerase chain reaction (AS-PCR) methods. These markers can be used as co-dominant markers that detect heterozygotes of the NtMLO genes at the seedling stage in back-crossed progenies, and will contribute to the simplification of breeding.

Isolation of a Male-Specific Molecular Marker and Development of a Genetic Sex Identification Technique in Spotted Knifejaw (Oplegnathus punctatus)

Sex-specific DNA markers are very helpful for identifying genetic sex and studying sex determination mechanisms in fish. To identify the sex-specific markers of spotted knifejaw (Oplegnathus punctatus), we performed a comparative analysis of the female and male genomes. In this study, an 18 bp insertion was identified in the male genome after verification by sequencing depth and PCR. An effective and rapid method based on PCR was then developed to identify the genetic sex. A male-female-shared primer pair and a male-specific primer were designed for PCR amplification to avoid false-negative phenomena. To examine the primers in practice, we utilized hundreds of spotted knifejaw fish from different groups to identify their genetic sex, and the results were consistent with their phenotypic sex. The male-specific DNA marker would be helpful for artificial breeding, Y chromosome assembly and further study of the sex determination mechanism. This study is the first to identify an effective sex-specific marker in spotted knifejaw.

A note on the larva of Chalcophora japonica chinensis (Coleoptera, Buprestidae) based on morphological characters and molecular data

Larvae of Chalcophora japonica chinensis Schaufuss, 1879 were collected from within dead trunks in Hubei Province, China, in February 2019. These specimens created an opportunity to provide the first description of the larval stage of this subspecies; The larva is described and illustrated based on morphological characters and DNA barcoding.

Genetic study of diversity and blast resistance in Ethiopian rice cultivars adapted to different ecosystems

Rice (Oryza sativa L.) has been considered one of the most important crops in Ethiopia. Landraces and improved accessions in Ethiopia were characterized on the basis of polymorphism data for SSR markers, and classified into two groups: I and II. Cluster I was further divided into two sub-clusters, Ia and Ib. Cluster Ia corresponded to Japonica-like type, Cluster Ib to Japonica type, and Cluster II to Indica type with some Indica-like type. Many landraces and improved varieties belonged to Cluster Ia. Superior landraces were included in Cluster Ib. Further categorization based on blast resistance demonstrated three groups: Clusters A, B1, and B2. Cluster A comprised accessions with relatively high resistance, whereas Clusters B1 and B2 included susceptible accessions. Most of the improved varieties were found in Cluster A. Superior landraces, X-Jigna classified into Ib or DNA type tended to be susceptible in Cluster B2 for blast resistance. These results demonstrated that traditional landraces preferred by farmers should be improved for disease resistance using blast-resistant varieties. In order to avoid hybrid sterility occurring in cross-hybridizing breeding between Indica and Japonica types, desirable parental accessions can be chosen within the same DNA cluster. The clustering information among accessions may be useful in breeding schemes for selection of counterparts in cross-breeding programs.

Transcriptome Comparison of Defense Responses in the Rice Variety 'Jao Hom Nin' Regarding Two Blast Resistant Genes, Pish and Pik

Jao Hom Nin (JHN) is a Thai rice variety with broad-spectrum resistant against rice blast fungus. JHN contains two rice blast resistant genes, Pish and Pik, located on chromosome 1 and on chromosome 11, respectively. To understand the blast resistance in JHN, the study of the defense mechanism related to the Pish and Pik genes is crucial. This study aimed to dissect defense response genes between the Pish and Pik genes using the RNA-seq technique. Differentially expressed genes (DEGs) of Pish and Pik backcross inbred lines were identified between 0 and 24 h after inoculation with rice blast spore suspension. The results showed that 1248 and 858 DEGs were unique to the Pish and Pik lines, respectively. The wall-associated kinase gene was unique to the Pish line and the zinc-finger-containing protein gene was unique to the Pik line. Pathogenicity-related proteins PR-4 and PR-10 were commonly found in both Pish and Pik lines. Moreover, DEGs functionally categorized in brassinosteriod, jasmonic acid, and salicylic acid pathways were detected in both Pish and Pik lines. These unique and shared genes in the Pish and Pik rice blast defense responses will help to dissect the mechanisms of plant defense and facilitate rice blast breeding programs.

A putative AGAMOUS ortholog is a candidate for the gene determining ease of dehulling in Tartary buckwheat (Fagopyrum tataricum)

Tartary buckwheat rice-type cultivars, which allow easy dehulling, lacked periclinal cell divisions that proceed underneath the epidermis in the proximity of ovary midribs in non-rice-type cultivars. The easy dehulling in these cultivars was associated with a G→A substitution in an AGAMOUS ortholog. Ease of dehulling in Tartary buckwheat (Fagopyrum tataricum) can affect the quality of its products. Tartary buckwheat cultivars that allow easy dehulling are called rice-type cultivars. The rice and non-rice hull types are determined by a single gene, but this gene is unclear. Here, we show that cells underneath the epidermis in the proximity of ovary midribs undergo periclinal cell divisions in non-rice-type cultivars but do not in a rice-type cultivar. The cells that arose from the periclinal cell divisions later underwent lignification, which should increase mechanical strength of hulls. In RNA sequencing, a partial mRNA of an AGAMOUS ortholog in Tartary buckwheat (FtAG) was found to be absent in the rice-type cultivar. Cloning of this gene revealed that this is a 42-bp deletion due to a G→A substitution at a splice acceptor site in the FtAG genomic region. In F2 progeny derived from a cross between non-rice-type and rice-type cultivars, all the rice-type plants exhibited the homozygous A/A allele at this site, whereas all the Tartary-type plants exhibited either the homozygous G/G allele or the heterozygous A/G allele. These results suggest that FtAG is a candidate for the gene that determines ease of dehulling in Tartary buckwheat. The DNA marker that we developed to distinguish the FtAG alleles can be useful in breeding Tartary buckwheat cultivars.

A QTL associated with high seed coat cracking rate of a leading Japanese soybean variety

Seed coat cracking in soybeans [Glycine max (L). Merr.] leads to commercial and agronomic losses. The Japanese elite soybean cultivar 'Fukuyutaka' is often used as a parent for breeding, but its high rate of seed coat cracking is an obstacle to its further use in breeding programs. To establish a DNA marker-assisted selection system for seed coat cracking, genetic factors related to high rates of seed coat cracking were surveyed, and a quantitative trait locus (QTL) with a stable effect on seed coat cracking in both years of a two-year replication experiment was detected on chromosome 20. Comparison of a set of near-isogenic lines (NILs) around this locus verified that the presence of the 'Fukuyutaka' allele significantly increased seed coat cracking in the kernel. The locus is located in a genomic region spanning 3.2 Mb. Marker-assisted selection for the locus will improve the selection efficiency of 'Fukuyutaka'-derived breeding populations.

Identification and Monitoring of Amomi Fructus and its Adulterants Based on DNA Barcoding Analysis and Designed DNA Markers

Amomi Fructus is one of the traditional medicines derived from the ripe fruits of the Zingiberaceae family of plants, which include Amomum villosum, A. villosum var. xanthioides, and A. longiligulare. Owing to their highly similar morphological traits, several kinds of adulterants of Amomi Fructus have been reported. Therefore, accurate and reliable methods of identification are necessary in order to ensure drug safety and quality. We performed DNA barcoding using five regions (ITS, matK, rbcL, rpoB, and trnL-F intergenic spacer) of 23 Amomi Fructus samples and 22 adulterants. We designed specific DNA markers for Amomi Fructus based on the single nucleotide polymorphisms (SNPs) in the ITS. Amomi Fructus was well separated from the adulterants and was classified with the species of origin based on the detected SNPs from the DNA barcoding results. The AVF1/ISR DNA marker for A. villosum produced a 270 bases amplified product, while the ALF1/ISF DNA marker produced a 350 bases product specific for A. longiligulare. Using these DNA markers, the monitoring of commercially distributed Amomi Fructus was performed, and the monitoring results were confirmed by ITS analysis. This method identified samples that were from incorrect origins, and a new species of adulterant was also identified. These results confirmed the accuracy and efficiency of the designed DNA markers; this method may be used as an efficient tool for the identification and verification of Amomi Fructus.

A new DNA marker CafLess-TCS1 for selection of caffeine-less tea plants

A clonal line of Camellia taliensis, 'Taliensis-akeme' has a recessive caffeine-less gene. To accelerate breeding of caffeine-less tea cultivars using this gene, DNA markers are indispensable for selecting heterozygotes that do not show a caffeine-less phenotype as parental lines. Therefore, we tried to determine the sequence of the six tea caffeine synthase (TCS) genes to search for polymorphisms and to prepare one of the TCS genes as a selection marker. Six TCS genes and the caffeine-less trait were mapped on the reference linkage map of tea. Strong linkage between the caffeine-less phenotype and TCS1 indicate that it is a promising candidate as a causative gene of the caffeine-less trait. We decided to use a three-nucleotide insertion in TCS1 that can be distinguished by sequencing as a selection marker named 'CafLess-TCS1'. Caffeine-less individuals appeared in the progeny population of caffeine-less heterozygous individuals selected using 'CafLess-TCS1'. These results confirmed that the developed 'CafLess-TCS1' will be an effective selection marker for breeding of caffeine-less tea cultivars.

Towards sex identification of Asian Palmyra palm (Borassus flabellifer L.) by DNA fingerprinting, suppression subtractive hybridization and de novo transcriptome sequencing

BACKGROUND

Asian Palmyra palm, the source of palm-sugar, is dioecious with a long juvenile period requiring at least 12 years to reach its maturity. To date, there is no reliable molecular marker for identifying sexes before the first bloom, limiting crop designs and utilization. We aimed to identify sex-linked markers for this palm using PCR-based DNA fingerprinting, suppression subtractive hybridization (SSH) and transcriptome sequencing.

METHODS

DNA fingerprints were generated between males and females based on RAPD, AFLP, SCoT, modified SCoT, ILP, and SSR techniques. Large-scale cloning and screening of SSH libraries and de novo transcriptome sequencing of male and female cDNA from inflorescences were performed to identify sex-specific genes for developing sex-linked markers.

RESULTS

Through extensive screening and re-testing of the DNA fingerprints (up to 1,204 primer pairs) and transcripts from SSH (>10,000 clones) and transcriptome data, however, no sex-linked marker was identified. Although de novo transcriptome sequencing of male and female inflorescences provided ∼32 million reads and 187,083 assembled transcripts, PCR analysis of selected sex-highly represented transcripts did not yield any sex-linked marker. This result may suggest the complexity and small sex-determining region of the Asian Palmyra palm. To this end, we provide the first global transcripts of male and female inflorescences of Asian Palmyra palm. Interestingly, sequence annotation revealed a large proportion of transcripts related to sucrose metabolism, which corresponds to the sucrose-rich sap produced in the inflorescences, and these transcripts will be useful for further understanding of sucrose production in sugar crop plants. Provided lists of sex-specific and differential-expressed transcripts would be beneficial to the further study of sexual development and sex-linked markers in palms and related species.

Development of a DNA marker for variety discrimination specific to 'Manten-Kirari' based on an NGS-RNA sequence in Tartary buckwheat (Fagopyrum tataricum)

To discriminate the trace-rutinosidase variety of Tartary buckwheat 'Manten-Kirari', we developed DNA markers based on RNA polymorphism. Specifically, we mapped 17.76 GB RNA sequences, obtained using HiSeq2000, to create 11,358 large contigs constructed de novo from 'Manten-Kirari' RNA derived from GS-FLX+ titanium. From these, we developed eight DNA markers corresponding to single- to four-nucleotide polymorphisms between 'Manten-Kirari' and 'Hokkai T8', which is representative of normal rutinosidase content varieties in Japan. Using these markers, 'Manten-Kirari' was discriminated from 'Hokkai T8' by eight markers, from major Tartary buckwheat varieties by three markers, and from common buckwheats by two markers. We also performed direct PCR from flour and dried noodle made with 'Manten-Kirari' and 'Hokkai T8'. Based on the results, the DNA markers developed are promising for discriminating 'Manten-Kirari'. This is the first study to develop a DNA marker to discriminate varieties in the Polygonaceae family including buckwheat species.

Marker-trait association for grain weight of spring barley in well-watered and drought environments

Climate change will increase the effect of drought stress which is one of major constrains for barley production and productivity in Egypt. Identification and development new cultivars having a high drought tolerance combined with a high yield are urgently needed. In this study, a set of 60 highly homozygous and diverse barley genotypes was evaluated in well-watered (N) and dry (D) environments for two successive seasons. Five yield traits were scored; plant height, spike length, days to flowering, grain yield per spike (GYPS), and thousand kernel weight (TKW). High genetic variation was found among genotypes in all studied traits under N and D. High heritability for all traits was observed in both seasons. The drought susceptibility index (DSI) for GYPS and TKW was estimated to determine the tolerant and susceptible genotypes in both seasons. As a result, four spring barley genotypes were considered drought tolerant for TKW and GYPS in both seasons. A set of ten single sequence repeats primers, developed from wheat genome, were tested in the 60 genotypes. All SSR primers had a high polymorphism among the genotypes producing 82 marker alleles. Single marker analysis was performed for DSI, TKW, and GYPS in both seasons. Twenty QTLs were found to be associated with low DSI and high GYPS and TKW in N and D. The marker alleles associated with the 20 QTL were screened in the four tolerant genotypes. PNBYT15 included only one marker allele associated with one QTL, while, SCYT-28 included six marker alleles controlling nine QTL. The high genetic variation and heritability for the studied traits indicated that these traits could be used for selection for high yielding and drought tolerance. The four drought tolerant genotypes can be used for a further breeding program to improve drought tolerance in barley.

Rapid DNA-genotyping system targeting ten loci for resistance to blast disease in rice

The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5% consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.

Effect of change from a determinate to a semi-determinate growth habit on the yield and lodging resistance of soybeans in the northeast region of Japan

Although an indeterminate growth habit is attractive to develop high-yield soybean varieties with higher number of pods (Glycine max (L). Merr.), lodging in indeterminate varieties remains a problem in Japan. As the semi-determinate varieties have shorter main stem length than the indeterminate varieties, this trait can be useful to improve varieties with high yield and low lodging risk. We introduced the genes Dt1 and Dt2, which regulate stem growth habit, into three determinate varieties by backcrossing and evaluated the resulting effects on yield and lodging tendency under four different growing environments. The yield and lodging degree of the semi-determinate and indeterminate lines were higher and more severe than those of the determinate lines. Despite the lower overall lodging score, the semi-determinate lines had marginally lower overall yield than that of the indeterminate lines. However, the effect of introduction of semi-determinate traits on yield and lodging degree was different in the three backgrounds, with the yield of semi-determinate lines being the highest and the difference in lodging degree between the semi-determinate and determinate lines being under 1.0 in one background. Therefore, semi-determinate growth habit has potential to develop high yielding varieties with low lodging risk.

DNA barcoding of flowering plants in Sumatra, Indonesia

The rapid conversion of Southeast Asian lowland rainforests into monocultures calls for the development of rapid methods for species identification to support ecological research and sustainable land-use management. Here, we investigated the utilization of DNA barcodes for identifying flowering plants from Sumatra, Indonesia. A total of 1,207 matK barcodes (441 species) and 2,376 rbcL barcodes (750 species) were successfully generated. The barcode effectiveness is assessed using four approaches: (a) comparison between morphological and molecular identification results, (b) best-close match analysis with TaxonDNA, (c) barcoding gap analysis, and (d) formation of monophyletic groups. Results show that rbcL has a much higher level of sequence recoverability than matK (95% and 66%). The comparison between morphological and molecular identifications revealed that matK and rbcL worked best assigning a plant specimen to the genus level. Estimates of identification success using best-close match analysis showed that >70% of the investigated species were correctly identified when using single barcode. The use of two-loci barcodes was able to increase the identification success up to 80%. The barcoding gap analysis revealed that neither matK nor rbcL succeeded to create a clear gap between the intraspecific and interspecific divergences. However, these two barcodes were able to discriminate at least 70% of the species from each other. Fifteen genera and twenty-one species were found to be nonmonophyletic with both markers. The two-loci barcodes were sufficient to reconstruct evolutionary relationships among the plant taxa in the study area that are congruent with the broadly accepted APG III phylogeny.

Dystroglycan 1: A new candidate gene for patellar luxation in Chihuahua dogs

Aim:

The objective of this study was to uncover new candidate genes related to patellar luxation (PL) in dogs to select for those with low susceptibility for breeding purposes.

Materials and Methods:

The inter simple sequence repeat (ISSR) technique was performed to construct DNA fingerprints of 61 Chihuahua dogs with PL and 30 healthy Chihuahua dogs. DNA polymorphisms were detected by comparing the sequences between the affected and unaffected dogs, using the pairwise alignments in MultAlin. Genotyping was performed using allele-specific polymerase chain reaction (AS-PCR). The association analysis of ISSR DNA fingerprints and genotypes or phenotypes was performed using the Chi-square (χ²) model and generalized linear model (GLM), respectively.

Results:

Two single nucleotide polymorphisms (SNPs), namely SNP1UBC811 (g.91175C>G) and SNP2UBC811 (g.92259T>C), were found in the intron of the Dystroglycan 1 (DAG1) gene, which was obtained using the PL-related marker UBC811 primer (p=0.02), and genotyped by AS-PCR. When investigated using the GLM, g.91175C>G had a significant association with PL (p=0.0424), whereas g.92259T>C did not have such an association (p=0.0959).

Conclusion:

DAG1 might be one of the genes related to PL in Chihuahuas and could aid the process of marker-assisted selection in genetic breeding for Chihuahua dogs without PL.

A new DNA marker of the TMIGD1 gene used to identify high fertilization rates in Tsaiya ducks (Anas platyrhynchos)

In a prior study, comparisons of individuals of Anas platyrhynchos with higher/lower reproductive performances showed that the expression of the transmembrane and immunoglobulin domain containing 1 (TMIGD1) gene significantly differed between the two groups. Here, we demonstrate that ducks with the TMIGD1 GG genotype have a significantly higher fertilization rate than other TMIGD1 genotypes. Primers designed based on the TMIGD1 sequence of Pekin duck were able to successfully amplify a TMIGD1 fragment from Tsaiya ducks, and sequencing results indicated that a single nucleotide polymorphism (SNP) of the TMIGD1 gene existed. We also developed a cost-effective method of restriction fragment length polymorphism. Using the above methods, ducks were classified into three genotypes. To identify the relationships between genotypes and traits, we recorded the ducks’ performance; to ensure the coverage of the entire duration of the fertile period, the egg collection period was extended to 18 days, and therefore, lower than usual fertilization rates were observed. Further assessment using a high-throughput system showed that the ducks with the GG genotype exhibited the highest fertilization rates among genotypes (P < 0.05). We suggest that TMIGD1 may affect the release of sperm protection factors from the female genital tract, and thus alter fertilization rate. In conclusion, the results of this study demonstrate that the TMIGD1 GG genotype can be used as a new DNA marker to identify animals with high fertilization rates at a young age, a process which could improve farming efficiency.

Selection criteria for SNP loci to maximize robustness of high-resolution melting analysis for plant breeding

DNA markers are useful for identifying genes and developing new genetic materials for breeding and genetic research. High-resolution melting (HRM) analysis can detect a single nucleotide polymorphism (SNP) in two polymerase chain reaction (PCR) fragments as a melting temperature (Tm) difference without additional experimental steps, such as gel electrophoresis. To design a method for developing reliable HRM markers that discriminate between homozygous alleles containing SNPs, we tested new evaluation indexes related to the thermodynamics of double-stranded DNA to find one that maximizes the difference in Tm values between PCR fragments. We found that differences in the change in Gibbs free energy (ΔG°) correlated with actual differences in Tm values. Optimization of the nearest neighboring nucleotide (NNN) of a SNP by nucleotide substitution in the primer and reducing the size of the PCR fragment both enlarged the actual differences in Tm. The genetic DNA markers we developed by NNN substitution, termed NNNs-HRM markers, could be precisely mapped within soybean chromosomes by linkage analysis. We developed a Perl script pipeline to enable the automatic design of a massive number of NNNs-HRM markers; these scripts are freely available and would be useful for practical breeding programs for other plant species.

MITE insertion-dependent expression of CitRKD1 with a RWP-RK domain regulates somatic embryogenesis in citrus nucellar tissues

BACKGROUND

Somatic embryogenesis in nucellar tissues is widely recognized to induce polyembryony in major citrus varieties such as sweet oranges, satsuma mandarins and lemons. This capability for apomixis is attractive in agricultural production systems using hybrid seeds, and many studies have been performed to elucidate the molecular mechanisms of various types of apomixis. To identify the gene responsible for somatic embryogenesis in citrus, a custom oligo-DNA microarray including predicted genes in the citrus polyembryonic locus was used to compare the expression profiles in reproductive tissues between monoembryonic and polyembryonic varieties. The full length of CitRKD1, which was identified as a candidate gene responsible for citrus somatic embryogenesis, was isolated from satsuma mandarin and its molecular function was investigated using transgenic 'Hamlin' sweet orange by antisense-overexpression.

RESULTS

The candidate gene CitRKD1, predominantly transcribed in reproductive tissues of polyembryonic varieties, is a member of the plant RWP-RK domain-containing protein. CitRKD1 of satsuma mandarin comprised two alleles (CitRKD1-mg1 and CitRKD1-mg2) at the polyembryonic locus controlling embryonic type (mono/polyembryony) that were structurally divided into two types with or without a miniature inverted-repeat transposable element (MITE)-like insertion in the upstream region. CitRKD1-mg2 with the MITE insertion was the predominant transcript in flowers and young fruits where somatic embryogenesis of nucellar cells occurred. Loss of CitRKD1 function by antisense-overexpression abolished somatic embryogenesis in transgenic sweet orange and the transgenic T₁ plants were confirmed to derive from zygotic embryos produced by self-pollination by DNA diagnosis. Genotyping PCR analysis of 95 citrus traditional and breeding varieties revealed that the CitRKD1 allele with the MITE insertion (polyembryonic allele) was dominant and major citrus varieties with the polyembryonic allele produced polyembryonic seeds.

CONCLUSION

CitRKD1 at the polyembryonic locus plays a principal role in regulating citrus somatic embryogenesis. CitRKD1 comprised multiple alleles that were divided into two types, polyembryonic alleles with a MITE insertion in the upstream region and monoembryonic alleles without it. CitRKD1 was transcribed in reproductive tissues of polyembryonic varieties with the polyembryonic allele. The MITE insertion in the upstream region of CitRKD1 might be involved in regulating the transcription of CitRKD1.

Complete Chloroplast Genome Sequences of Four Meliaceae Species and Comparative Analyses

The Meliaceae family mainly consists of trees and shrubs with a pantropical distribution. In this study, the complete chloroplast genomes of four Meliaceae species were sequenced and compared with each other and with the previously published Azadirachta indica plastome. The five plastomes are circular and exhibit a quadripartite structure with high conservation of gene content and order. They include 130 genes encoding 85 proteins, 37 tRNAs and 8 rRNAs. Inverted repeat expansion resulted in a duplication of rps19 in the five Meliaceae species, which is consistent with that in many other Sapindales, but different from many other rosids. Compared to Azadirachta indica, the four newly sequenced Meliaceae individuals share several large deletions, which mainly contribute to the decreased genome sizes. A whole-plastome phylogeny supports previous findings that the four species form a monophyletic sister clade to Azadirachta indica within the Meliaceae. SNPs and indels identified in all complete Meliaceae plastomes might be suitable targets for the future development of genetic markers at different taxonomic levels. The extended analysis of SNPs in the matK gene led to the identification of four potential Meliaceae-specific SNPs as a basis for future validation and marker development.

High-resolution mapping and characterization of xa42, a resistance gene against multiple Xanthomonas oryzae pv. oryzae races in rice (Oryza sativa L.)

Improvement of resistance against rice bacterial blight (BB) disease is an important breeding strategy in breeding programs across the world, especially in Africa and southern Asia where BB is more prevalent. This report describes a high-resolution map and characterization of xa42 at XA42 locus, a rice BB resistance gene in XM14, a mutant line originating from IR24. The candidate gene region was narrowed down from 582 kb, which had been obtained in our previous study, to 57 kb. XM14 shows brown spots in its leaves like lesion mimic mutants. This line also shows a shorter stature than the original cultivar IR24. In XA42 gene segregating populations, homozygotes of xa42 allele were consistently resistant to the six Japanese Xanthomonas oryzae pv. oryzae races used for this study. They also showed brown spots and markedly short stature compared with the other genotypes, suggesting that xa42 gene exhibits pleiotropic effects.

Development of basic technologies for improvement of breeding and cultivation of Japanese gentian

Japanese gentians are the most important ornamental flowers in Iwate Prefecture and their breeding and cultivation have been actively conducted for half a century. With its cool climate and large hilly and mountainous area, more than 60% of gentian production in Japan occurs in Iwate Prefecture. Recent advances in gentian breeding and cultivation have facilitated the efficient breeding of new cultivars; disease control and improved cultivation conditions have led to the stable production of Japanese gentians. Molecular biology techniques have been developed and applied in gentian breeding, including the diagnosis of viral diseases and analysis of physiological disorders to improve gentian production. This review summarizes such recent approaches that will assist in the development of new cultivars and support cultivation. More recently, new plant breeding techniques, including several new biotechnological methods such as genome editing and viral vectors, have also been developed in gentian. We, therefore, present examples of their application to gentians and discuss their advantages in future studies of gentians.

Application of DNA markers for discrimination between Japanese and Australian Wagyu beef

The objective of this study was to discriminate between original Japanese and Australian Wagyu beef, which is sold in the Singapore markets, using six previously developed DNA markers. To effectively evaluate the six markers for breed identification, the probability of identification as Australian Wagyu beef was calculated based on the estimated allele frequencies using 130 Australian Wagyu individuals. The combined use of six markers would allow the discrimination of Australian Wagyu beef with an estimated probability of 0.776. The probability to discriminate Australian Wagyu from Japanese Wagyu beef was sufficiently high. In addition, Australian Wagyu has maternal mitochondrial DNA of Bos indicus cattle with moderate high frequency of 0.377. The DNA marker system could also be used as a deterrent force against false sales, and contribute to the reduction and prevention of incorrect or falsified labeling of beef.

A Review of Salivary Biomarker: A Tool for Early Oral Cancer Diagnosis

The oral squamous cell carcinoma (OSCC) is one of the most common epithelial malignancies with significant morbidity and mortality. Recent observations indicate that the clinical and histological appearance of oral mucosa may not truly depict the damage occurring at the genetic level. This phenotypic and genotypic disparity may account in part for the failure to establish effective screening and surveillance protocols, based on the traditional clinical and microscopic examination. The tumor markers are playing an increasingly important role in cancer detection and management. These laboratory-based tests are potentially useful in screening for early malignancy, aiding in cancer diagnosis, determining prognosis, surveillance following curative surgery for cancer, up-front predicting drug response or resistance, and monitoring therapy in advanced disease. A systematic review of the literature was performed based on the English titles listed in the PubMed, EBSCO, Cochrane, Science Direct, ISI web Science, and SciELO databases using the keywords. Abstracts and full-text articles were assessed. This article may help to identify the potential biomarkers for screening and the molecular pathology analysis in the high-risk patients with the OSCC.

Rapid identification of apple (Malus×domestica Borkh.) S alleles using sequencing-based DNA marker APPLid

All apple cultivars harbor the trait called self-incompatibility. Self-incompatibility represents that the pistils of the flowers are not successfully fertilized with own, the same cultivar's pollens. Compatibility or incompatibility of apple flowers are determined by S alleles. For example, the most popular apple cultivar 'Fuji' possesses the S₁ and S₉ alleles (S₁S₉ ). Thus, 'Fuji' is incompatible with S₁S₉ cultivars, but is compatible with the cultivars possessing different combinations of S alleles such as S₂S₇ and S₁S₇ . Apple S alleles have been identified by performing a series of allele-specific PCR amplifications, to detect more than ten different S alleles separately. Here, we developed a new type of sequencing-based DNA marker of the apple S-RNase gene, which identifies S alleles. This DNA marker was named APPLid (apple S-allele identifier). A 53-base region in the first coding sequence of S-RNase is the target of APPLid sequencing. Variation in nucleotide sequences in this APPLid sequence enables allele identifications. This region is amplified from apple genomic DNA by using a pair of degenerate primers. The forward primer is attached with 'DS5 adaptor.' After PCR amplification, electrophoresis and gel extraction of 177-bp DNA fragments, APPLid sequence is determined by direct sequencing with a sequencing primer. The APPLid sequences of 20 apple cultivars completely matched their S alleles, which include triploid cultivars. In conclusion, APPLid identifies apple S alleles (S₁ , S₂ , S₃ , S₄ , S₅ , S₇ , S₉ , S₁₀ , S₂₀ , S₂₄ , S₂₅ , S₂₆ , S₂₇ and S₂₈ , so far) just by a single sequencing analysis.