Molecular Marker-assisted Selection Research Articles

New markers for flowering-time selection in sweet cherry

Sweet cherry (Prunus avium L.) is a fruit tree in the Rosaceae family grown worldwide for its tasty fruit. However, its yield may be threatened in warmer growing regions by insufficient dormancy, which usually occurs in late-blooming genotypes. Conversely, in cold regions, the yield is threatened by late spring frosts, especially for early flowering cultivars. It is therefore necessary to breed cultivars adapted to local weather conditions and avoid potential crop losses. New markers associated with the beginning of flowering were sought to enable molecular marker-assisted selection of genotypes tailored for different climatic conditions. Previously whole-genome sequenced 298 sweet cherry genotypes with nine years of phenotypic evaluation provided the basis for a genome-wide association study that allowed the identification of 163 single nucleotide polymorphisms and indels associated with flowering time, located on all sweet cherry chromosomes. This study confirmed the previously predicted polygenic basis of the trait. Three markers suitable for selection of late-blooming genotypes and one for early-blooming genotypes were selected and validated using independent 128 sweet cherry hybrids from different crossings. Individual markers for late beginning of flowering were able to select genotypes flowering at least three days after the reference (i.e. the earliest flowering) cultivar 'Kišiněvskaja'. Accumulation of preferred allele combinations for all three late-blooming markers has a synergistic effect, indicating delay of flowering 7.1 days after the reference cultivar on average. The marker for early beginning of flowering identified accessions flowering maximally five days after the earliest flowering reference cultivar 'Kišiněvskaja'. All four markers were integrated into a single base extension assay to help breeders with prediction of beginning of flowering for their breeding materials and cultivars.

Applications of Molecular Marker Implementation for Enhanced Oilseed Breeding through Marker-Assisted Selection (Mas)

Oilseed crops are fundamental for various industrial and food purposes, necessitating advancements in breeding strategies to meet growing demands. Molecular markers and Marker-Assisted Selection (MAS) have emerged as powerful tools in oilseed crop improvement. This review explores the diverse applications of molecular markers and MAS in oilseed crops, highlighting their significance in enhancing breeding efficiency and genetic gains. The primary aim of this review is to provide a comprehensive overview of the application of molecular markers and MAS in oilseed crop breeding programs. Specifically, it aims to synthesize existing literature and case studies to elucidate the methodologies, advancements, and outcomes associated with the integration of molecular markers and MAS in oilseed crop improvement. The review highlights significant advancements in the application of molecular markers and MAS in oilseed crop breeding. Molecular markers have been extensively utilized for trait mapping, genetic diversity analysis, and selection of desirable genotypes with traits such as high oil content, disease resistance, and abiotic stress tolerance. Integration with conventional breeding methods has facilitated the development of elite oilseed crop varieties with improved agronomic performance and stress resilience. In conclusion, molecular markers and MAS represent valuable tools for accelerating oilseed crop breeding programs. Their integration has led to increased breeding efficiency, precision, and genetic gains. However, challenges such as marker validation, cost-effectiveness, and trait complexity remain to be addressed. Future research efforts should focus on refining marker technologies, enhancing trait mapping studies, and promoting the adoption of MAS in oilseed crop breeding to ensure sustainable production and global food security.

The development and utilization of two SCAR markers linked to the resistance of banana (Musa spp. AAA) to Fusarium oxysporum f. sp. cubense race 4

Banana (Musa spp.) production worldwide is seriously threatened by Fusarium wilt caused by Fusarium oxysporum f. sp. cubense (Foc). The best way to control this disease is to grow resistant cultivars. However, it requires large-scale field evaluations and labor- and time-consuming to obtain disease-resistant germplasm. Development of early, reliable, and reproducible selection strategies are considered as the efficient approach which could speed up the selection procedure. In this study, two pairs of sequence-related amplified polymorphism (SRAP) primers related to banana Foc resistance/susceptibility were screened from 100 pairs of random primers. Correspondingly, two pairs of sequence characterized amplified region (SCAR) markers (namely SC4-F/SC4-R and SC14-F/SC14-R, respectively) were successfully generated from these two SRAP markers using 30 cultivars either resistant or susceptible to Foc. Both SCAR markers were located in mitochondrion genome and showed discriminatory power of 96.67% and 100%, respectively. Mitochondrial proteins possibly play a very important role in banana resistance to Foc. In additional, these two SCAR markers were employed simultaneously to screen potential resistant germplasm from 53 accessions with unknown resistance to Foc, and the results revealed a consistency of 83.0% with each other, further indicating their high reliability and reproducibility. These results suggest that both SCAR markers could be used in molecular marker-assisted selection for banana germplasm resistant to Fusarium.

Fine-mapping and primary analysis of candidate genes associated with seed coat color in mung bean (Vignaradiata L.)

Seed coat color affects the appearance and commodity quality of mung beans (Vigna radiata L.). The substances that affect mung bean seed coat color are mainly flavonoids, which have important medicinal value. Mapping the seed coat color gene in mung beans would help develop new varieties and improve their value. In this study, an F2 mapping population consisting of 546 plants was constructed using Jilv9 (black seed coat) and BIS9805 (green seed coat). Using bulk segregated analysis (BSA) sequencing and the kompetitive allele-specific PCR (KASP) markers, the candidate region related to seed coat color was finally narrowed to 0.66 Mb on Chr.4 and included eight candidate genes. Combined transcriptome and metabolome analyses showed that three of the eight candidate genes (LOC106758748, LOC106758747, and LOC106759075) were differentially expressed, which may have caused the differences in flavonoid metabolite content between Jilv9 and BIS9805. These findings could provide a research basis for cloning genes related to the seed coat color and accelerate molecular marker-assisted selection breeding in mung beans.

Dominance complementation of parental heading date alleles of Hd1, Ghd7, DTH8, and PRR37 confers transgressive late maturation in hybrid rice.

Rice (Oryza sativa L.) is a short-day plant whose heading date is largely determined by photoperiod sensitivity (PS). Many parental lines used in hybrid rice breeding have weak PS, but their F1 progenies have strong PS and exhibit an undesirable transgressive late-maturing phenotype. However, the genetic basis for this phenomenon is unclear. Therefore, effective methods are needed for selecting parents to create F1 hybrid varieties with the desired PS. In this study, we used bulked segregant analysis with F1 Ningyou 1179 (strong PS) and its F2 population, and through analyzing both parental haplotypes and PS data for 918 hybrid rice varieties, to identify the genetic basis of transgressive late maturation which is dependent on dominance complementation effects of Hd1, Ghd7, DTH8, and PRR37 from both parents rather than from a single parental genotype. We designed a molecular marker-assisted selection system to identify the genotypes of Hd1, Ghd7, DTH8, and PRR37 in parental lines to predict PS in F1 plants prior to crossing. Furthermore, we used CRISPR/Cas9 technique to knock out Hd1 in Ning A (sterile line) and Ning B (maintainer line) and obtained an hd1-NY material with weak PS while retaining the elite agronomic traits of NY. Our findings clarified the genetic basis of transgressive late maturation in hybrid rice and developed effective methods for parental selection and gene editing to facilitate the breeding of hybrid varieties with the desired PS for improving their adaptability.

Identification of SNPs and candidate genes associate with growth performance in all-female mandarin fish (Siniperca chuatsi) by a genome-wide association study

The all-female mandarin fish (Dinggui I, Siniperca Chuatsi) was recently approved by Ministry of Agriculture and Rural Affairs of the People's Republic of China as a new strain of mandarin fish (GS-04-001-2021). Select breeding of fast-growing lines is an important goal of the mandarin fish industry. However, single nucleotide polymorphisms (SNPs) associated with growth of Dinggui I mandarin fish remains unclear. Therefore, a genome-wide association study (GWAS) was performed on 5 growth traits (body weight, body length, whole length, body height and body thickness) of 192 mandarin fish. A total of 49,940 SNPs were identified by ddRAD-seq. Among them, a total of 6 significant SNPs were detected on multiple chromosomes. The proportion of phenotypic variance explained for these SNPs ranged from 9.66% to 19.47% for growth traits. Specifically, 4 SNPs were associated with all traits. Several candidate genes (AKT2, CCNT2, EPB41L2 and CAMKMT) were identified based on these SNPs. The loci were verified in 100 individuals, indicating the reliability of candidate SNPs. Our results contribute to understanding of growth traits and the development of molecular marker-assisted selection in all-female mandarin fish.

Determining the nutritional values of new corn varieties on pigs and broilers.

The objective of this study was to evaluate the nutritional values of three new corn varieties (high-iron corn, cadmium-resistant corn, low-phytate phosphorus corn) cultivated with molecular marker-assisted selection breeding technique fed to growing pigs and broilers. Exp. 1 was conducted to compare the nutritional values of high-iron corn, high-chromium corn, low-phytate phosphorus corn and conventional corn fed to growing pigs based on a 15 × 2 Youden square design. Exp.2 was conducted to compare the nutritional values of high-iron corn, low-phytate phosphorus corn and conventional corn fed to broilers based on a completely randomized design. Parameters including nutrient digestibility, available energy and amino acids, and mineral deposition were measured. The results shows that the iron content in the high-iron corn and the cadmium content in the cadmium-resistant corn were 29.608 mg/kg and 0.0057 mg/kg, respectively, both were greater than those in the other three kinds of corns. When fed to growing pigs, the neutral detergent fiber digestibility of the high-iron corn group was lower than that of the conventional corn group (p < 0.05), and the acid detergent fiber digestibility of the high-iron group and the low-phytate phosphorus corn group was lower than that of the conventional corn group (p < 0.01). In addition, the digestible energy value of the high-iron corn in growing pigs was lower than that of the conventional corn (p < 0.05). When fed to broilers, it was observed that the tibia length of the low-phytate phosphorus corn group and the high-iron corn group was lower than that of the conventional corn group (p < 0.05). Moreover, the iron emission in feces of broilers fed the low-phytate phosphorus corn was lower than those fed the conventional corn and the high-iron corn (p < 0.05). In conclusion, modern breeding techniques could provide new plant ingredients which have potential benefits to pig and broiler production, but the comprehensive effects may be better when applied to growing pigs considering growth performance and environment effects. The breeding techniques related to the current study rarely changed the available energy values of the corn in growing pigs and broilers.

Single nucleotide polymorphism SNP19140160 A > C is a potential breeding locus for fast-growth largemouth bass (Micropterus salmoides).

Largemouth bass (Micropterus salmoides) has significant economic value as a high-yielding fish species in China's freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F1 generation of a largemouth bass population. We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b, respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F1 generation population (703.86g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36g). Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.

Polymorphism in IGFALS gene and its association with scrotal circumference in Hu lambs

Scrotal circumference is an important reproductive index of breeding rams, which has a high genetic correlation with ejaculation volume and semen quality. In this study, the scrotal circumference of 1353 male Hu sheep at different stages of development was measured and descriptive statistical analysis was performed. The results showed that the coefficient of variation of scrotal circumference at each stage was greater than 10%, and its heritability were moderately to high, ranging from 0.318 to 0.719. We used PCR amplification and Sanger sequencing to scan the polymorphisms of the IGFALS gene, and performed association analysis with the circumference of the scrotum at different stages. We identified a synonymous mutation g.918 G > C in exon 1 of the IGFALS gene, and this mutation was significantly associated with scrotal circumference at 100, 120, 140, 160 and 180 days (p < 0.05). Therefore, IGFALS gene polymorphism can be used as a molecular marker affecting scrotal circumference of Hu sheep, which can provide a reference for future molecular marker-assisted selection of scrotal circumference in sheep.

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves.

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3'H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.

Genome-wide association study of kernel colour traits and mining of elite alleles from the major loci in maize

BackgroundMaize kernel colour is an important index for evaluating maize quality and value and mainly entails two natural pigments, carotenoids and anthocyanins. To analyse the genetic mechanism of maize kernel colour and mine single nucleotide polymorphisms (SNPs) related to kernel colour traits, an association panel including 244 superior maize inbred lines was used to measure and analyse the six traits related to kernel colour in two environments and was then combined with the about 3 million SNPs covering the whole maize genome in this study. Two models (Q + K, PCA + K) were used for genome-wide association analysis (GWAS) of kernel colour traits.ResultsWe identified 1029QTLs, and two SNPs contained in those QTLs were located in coding regions of Y1 and R1 respectively, two known genes that regulate kernel colour. Fourteen QTLs which contain 19 SNPs were within 200 kb interval of the genes involved in the regulation of kernel colour. 13 high-confidence SNPs repeatedly detected for specific traits, and AA genotypes of rs1_40605594 and rs5_2392770 were the most popular alleles appeared in inbred lines with higher levels. By searching the confident interval of the 13 high-confidence SNPs, a total of 95 candidate genes were identified.ConclusionsThe genetic loci and candidate genes of maize kernel colour provided in this study will be useful for uncovering the genetic mechanism of maize kernel colour, gene cloning in the future. Furthermore, the identified elite alleles can be used to molecular marker-assisted selection of kernel colour traits.

Relationships between the mutations of the goat GATA binding protein 4 gene and growth traits

Osteogenesis is a complex multilevel process regulated by multiple genes. The GATA binding protein 4 (GATA4) gene has been extensively studied for its pivotal role in bone genesis and bone differentiation. However, its relationship with the growth traits of Shaanbei white cashmere (SBWC) and Guizhou black (GB) goats remains unclear. This work aims to investigate the potential influence of genetic mutations in the GATA4 gene on the growth traits goats. Thus, two Insertion/deletion (InDel) polymorphisms (8-bp-InDel and 9-bp-InDel) were screened and detected in a total of 1161 goats (including 980 SBWC goats and 181 GB goats) using PCR and agarose gel electrophoresis. The analyses revealed that there were two genotypes (ID and DD) for these two loci. In SBWC goats, 8-bp-InDel and 9-bp-InDel loci were significantly associated with heart girth (HG) and hip width (HW). Notably, individuals with DD genotype of 8-bp-InDel locus were superior while those with DD genotype of 9-bp-InDel locus were inferior. Correlation analyses of the four combined genotypes revealed significant associations with cannon circumference (CC), body height (BH), HG and HW. This work provides a foundation for the application of molecular marker-assisted selection (MAS) in goat breeding programs. Furthermore, the findings highlight the potential of the GATA4 gene and its genetic variations as valuable indicators for selecting goats with desirable growth traits.

A High-Resolution Linkage Map Construction and QTL Analysis for Morphological Traits in Anthurium (Anthurium andraeanum Linden).

Anthurium andraeanum Linden is a prominent ornamental plant belonging to the family Araceae and is cultivated worldwide. The morphology characteristics are crucial because they significantly impact ornamental values, commercial properties, and the efficiency of space utilization in production. However, only a few related investigations have been conducted in anthurium to date. In this study, an F1 genetic segregation population containing 160 progenies was generated through hybridization between potted and cut anthurium varieties. Fifteen morphological traits were assessed and revealed substantial levels of genetic variation and widespread positive correlation. Based on specific length amplified fragment (SLAF) sequencing technology, 8171 single nucleotide polymorphism (SNP) markers were developed, and the high-density linkage map of 2202.27 cM in length distributed on 15 linkage groups was constructed successfully, with an average distance of 0.30 cM. Using the inclusive composite interval mapping (ICIM) method, 59 QTLs related to 15 key morphological traits were successfully identified, which explained phenotypic variance (PVE) ranging from 6.21% to 17.74%. Thirty-three of those associated with 13 traits were designated as major QTLs with PVE > 10%. These findings offer valuable insights into the genetic basis of quantitative traits and are beneficial for molecular marker-assisted selection (MAS) in anthurium breeding.

Development of Single-Segment Substitution Lines and Fine-Mapping of qSPP4 for Spikelets Per Panicle and qGW9 for Grain Width Based on Rice Dual-Segment Substitution Line Z783.

Single segment substitution line (SSSL) libraries are an ideal platform for breeding by design. To develop SSSLs-Xihui18 covering the whole genome, a novel rice chromosome segment substitution line (CSSL), Z783, carrying two substitution segments (average length of 6.55 Mb) on Chr.4 and Chr.9 was identified, which was a gap in the library previously. Z783 was developed from the progeny of recipient "Xihui18" (an indica restorer line) and donor "Huhan3" (a japonica cultivar) by advanced backcross combined molecular marker-assisted selection (MAS). It displayed multiple panicles and less spikelets and wide grains. Then, a F2 population derived from Xihui18/Z783 was used to map quantitative trait loci (QTLs) for yield-related traits by the mixed linear model method. Nine QTLs were detected (p < 0.05). Furthermore, three SSSLs were constructed by MAS, and all 9 QTLs could be validated, and 15 novel QTLs could be detected by these SSSLs by a one-way ANOVA analysis. The genetic analysis showed that qSSP4 for less spikelets and qGW9 for wide grain all displayed dominant gene action in their SSSLs. Finally, qSSP4 and qGW9 were fine-mapped to intervals of 2.75 Mb and 1.84 Mb, on Chromosomes 4 and 9, respectively. The results lay a solid foundation for their map cloning and molecular breeding by design.

Genome-wide association study on resistance of cultivated soybean to Fusarium oxysporum root rot in Northeast China

BackgroundFusarium oxysporum is a prevalent fungal pathogen that diminishes soybean yield through seedling disease and root rot. Preventing Fusarium oxysporum root rot (FORR) damage entails on the identification of resistance genes and developing resistant cultivars. Therefore, conducting fine mapping and marker development for FORR resistance genes is of great significance for fostering the cultivation of resistant varieties. In this study, 350 soybean germplasm accessions, mainly from Northeast China, underwent genotyping using the SoySNP50K Illumina BeadChip, which includes 52,041 single nucleotide polymorphisms (SNPs). Their resistance to FORR was assessed in a greenhouse. Genome-wide association studies utilizing the general linear model, mixed linear model, compressed mixed linear model, and settlement of MLM under progressively exclusive relationship models were conducted to identify marker-trait associations while effectively controlling for population structure.ResultsThe results demonstrated that these models effectively managed population structure. Eight SNP loci significantly associated with FORR resistance in soybean were detected, primarily located on Chromosome 6. Notably, there was a strong linkage disequilibrium between the large-effect SNPs ss715595462 and ss715595463, contributing substantially to phenotypic variation. Within the genetic interval encompassing these loci, 28 genes were present, with one gene Glyma.06G088400 encoding a protein kinase family protein containing a leucine-rich repeat domain identified as a potential candidate gene in the reference genome of Williams82. Additionally, quantitative real-time reverse transcription polymerase chain reaction analysis evaluated the gene expression levels between highly resistant and susceptible accessions, focusing on primary root tissues collected at different time points after F. oxysporum inoculation. Among the examined genes, only this gene emerged as the strongest candidate associated with FORR resistance.ConclusionsThe identification of this candidate gene Glyma.06G088400 improves our understanding of soybean resistance to FORR and the markers strongly linked to resistance can be beneficial for molecular marker-assisted selection in breeding resistant soybean accessions against F. oxysporum.

Genome-wide association analysis of time to heading and maturity in bread wheat using 55K microarrays.

To investigate the genetic mechanisms underlying the reproductive traits (time to flowering and maturity) in wheat and identify candidate genes associated, a phenotypic analysis was conducted on 239 wheat accessions (lines) from around the world. A genome-wide association study (GWAS) of wheat heading and maturity phases was performed using the MLM (Q+K) model in the TASSLE software, combined with the Wheat 55K SNP array. The results revealed significant phenotypic variation in heading and maturity among the wheat accessions across different years, with coefficients of variation ranging from 0.96% to 1.97%. The phenotypic data from different years exhibited excellent correlation, with a genome-wide linkage disequilibrium (LD) attenuation distance of 3 Mb. Population structure analysis, evolutionary tree analysis, and principal component analysis indicated that the 239 wheat accessions formed a relatively homogeneous natural population, which could be divided into three subgroups. The GWAS results identified a total of 293 SNP marker loci that were significantly associated with wheat heading and maturity stages (P ≤ 0.001) in different environments. Among them, nine stable SNP marker loci were consistently detected in multiple environments. These marker loci were distributed on wheat chromosomes 1A、1B、2D、3A、5B、6D and 7A. Each individual locus explained 4.03%-16.06% of the phenotypic variation. Furthermore, through careful analysis of the associated loci with large phenotypic effect values and stable inheritance, a total of nine candidate genes related to wheat heading and maturity stages were identified. These findings have implications for molecular marker-assisted selection breeding programs targeting specific wheat traits at the heading and maturity stages. In summary, this study conducted a comprehensive GWAS of wheat heading and maturity phases, revealing significant associations between genetic markers and key developmental stages in wheat. The identification of candidate genes and marker loci provides valuable information for further studies on wheat breeding and genetic improvement targeted at enhancing heading and maturity traits.

Identification and validation of major-effect quantitative trait locus QMS-5B associated with male sterility in photo-thermo-sensitive genic male sterile wheat.

QMS-5B, a major QTL for photo-thermo-sensitive genic male sterility in wheat, was fine mapped in a 2.15Mb region harboring a serine/threonine protein kinase gene TraesCS5B03G0887500, which was the most likely candidate gene. Genic male sterility is an essential trait in the utilization of heterosis and hybrid seed production for wheat. Currently, genic male sterile genes have been reported in wheat mutants, but the sterile genes controlling photo-thermo-sensitive genic male sterility in wheat have not been studied systematically. Here, 235 doubled haploid lines derived from a cross between photo-thermo-sensitive genic male sterile line BS462 and its restorer line CP279 were used to map male sterile gene by GenoBaits® Wheat 100K Panel, bulked segregant exome sequencing (BSE-Seq) and wheat 660K array. As a result, the major stable QTL on chromosome 5B, QMS-5B, was identified in all four environments, accounting for 7.3-36.4% of the phenotypic variances. Ulteriorly, QMS-5B was delimited to an approximate 2.15Mb physical interval between KASP-5B5 and KASP-5B6 using kompetitive allele-specific PCR (KASP) markers. Within the interval, twenty-nine high-confidence genes were predicted according to Chinese Spring RefSeq v2.1. TraesCS5B03G0887500, encoding a serine/threonine protein kinase, was identified as the most likely candidate gene for QMS-5B based on weighted gene co-expression network analysis. Expression analysis confirmed that TraesCS5B03G0887500 was significantly differentially expressed in anthers of BS462 and CP279 at different stages under fertile and sterile environments. In addition, flanking KASP marker KASP-5B6 can effectively genotype male sterile lines and restorer lines, and can be used for molecular marker-assisted selection. This study provides insights into for exploring the mechanism of photo-thermo-sensitive genic male sterility in wheat.

Recent Advances in Natural Deastringency and Genetic Improvement of Chinese PCNA Persimmon (Diospyros kaki)

Persimmon (Diospyros kaki) is a worldwide fruit cultivated mainly in the East Asia, Mediterranean, Caucasus, Latin America, and Oceania regions. This fruit contains abundant proanthocyanidins (PAs, also called condensed tannins), whose biosynthesis is the main cause of fruit astringency. As the original centre and top producing country, China has discovered a unique type with desirable natural deastringency, the Chinese pollination-constant non-astringent (C-PCNA) persimmon. Studies have revealed that the C-PCNA trait is controlled by a single and dominant locus, which differs from that of another type, the Japanese PCNA type, with recessive loci. In the C-PCNA type, accumulating evidence has shown that the astringency removal process involves two pathways (“dilution effect” and “coagulation effect”). Moreover, molecular marker-assisted selection (MAS) for the natural deastringency trait locus in C-PCNA has been used to test the non-astringency/astringency trait of hybrid offspring at the seedling stage. Importantly, persimmon can bear male flowers, female flowers, and perfect flowers, but sex-linked MAS has been developed for female-only persimmon. This sex-linked MAS, together with astringency-linked MAS and embryo rescue technology, may even shorten the conventional cross-breeding period of about 2–3 years. In addition, recently studies have established a stable genetic transformation system for persimmon transgenic improvement. Despite these efforts, how synthetic PAs and metabolism pathways lead to a deastringent trait remains unclear for persimmon. Thus, our review summarizes the latest research progress on the natural deastringency mechanism in C-PCNA, and we provide a new viewpoint for the genetic improvement of persimmon breeding in China.

QTL mapping in sesame (Sesamum indicum L.): A review.

Sesame (Sesamum indicum L.) is an important oilseed crop used for food, feed, medicinal, and industrial applications. Inherently low genetic yield potential and susceptibility to biotic and abiotic stresses contribute to low productivity in sesame. Development of stress resistant varieties coupled with high yield is a viable option to raise the genetic potential of sesame. Conventional phenotype-based breeding methods have made an important role in the last couple of decades by developing several sesame varieties with improved quality, yield, and tolerance to biotic and abiotic stresses. However, due to adverse environmental effects, time consuming to develop new variety, and low genetic gain, conventional phenotype-based approach is not adequate to satisfy the rising population growth. In this context, advanced method of genotype selection via modern techniques of biotechnology plays essential roles in reducing the constraints and boosting sesame production to satisfy the huge demand. In line to this, quantitative trait loci (QTL) mapping is considered as a promising method to address the problems of sesame breeding. Previously, huge data have been generated in the practical use of QTL for sesame improvement. Therefore, this paper aims to review recent advances in the area of QTL mapping for yield and yield related traits in sesame for enhancing and sustaining sesame production. In this section, we present an intensive review on the identification and mapping of the most desirable potential candidate genes/QTLs associated with desirable traits. Moreover, this review focuses on the major QTL regions and/or potential candidate genes and associated molecular markers that could provide potential genetic resources for molecular marker-assisted selection and further cloning of functional genes for yield and yield-related traits as well as various biotic and abiotic stress tolerances. Finally, the summarized QTL mapping data shed light on future directions for enhanced sesame breeding programs.

Application of a High-Density Single Nucleotide Polymorphism Genetic Map in Mapping Quantitative Trait Loci of Early-Maturing Traits in Upland Cotton

(1) Background: Mapping QTLs for early-maturing traits is necessary for the development of early-maturing variety breeding. (2) Methods: In this research, a high-density genetic map (HDGM) was constructed using an F2 population with 100 individuals and single nucleotide polymorphism markers (SNPs) developed using the genotyping-by-sequencing (GBS) method. (3) Results: The HDGM, which covered a total distance of 3167.14 cM, harbored 5454 SNPs with an average marker interval of 0.58 cM. In total, 18 QTLs for four early-maturing characters were detected and explained 11.6–46.4% of phenotypic variation (PV). Two QTLs of the whole growing period (WGP) and height of the node of the first fruiting branch (HNFFB) were identified as stable QTLs. In total, 125 candidate genes were identified in the confidence intervals of these stable QTLs. Presumably, Gh_D03G0857 may play an important role in regulating earliness. (4) Conclusions: This research will provide new information about fine mapping of QTLs for earliness traits, molecular marker assisted selection (MAS) of earliness traits, and pyramiding breeding as well.