Rapid Characterization of the Genetic Loci Controlling Commodity Traits of Chinese Hami Melon (Cucumis melo var. Saccharinensis Naud.) through Multiplexed Shotgun Genotyping

The genetic architecture and the genetic loci controlling commodity traits in this Hami melon have not been characterized. Multiplexed shotgun genotyping (MSG) was used to genotype an F2 population of 370 Chinese Hami melon progeny. A total of 47,609 single nucleotide polymorphism (SNP) markers were obtained after strict filtering. Thebins were used to construct a genetic linkage map with a total length of 1572.954 cM. Quantitative trait locus (QTL) analysis revealed that fruit color was controlled by one major gene about 2 Mb region on chr09, while exocarp color (EC) was controlled by one major gene about 1.9 Mb on chr04, and skin spotting was controlled by two dominant genes, one in the same region of chr04as the EC QTL and the other in the 1031.05 kb region on chr02. Two major QTLs on chr03 and chr05 were related pleiotropically to several quantitative fruit traits, namely, edge sugar content (ES), center sugar content (CS), fruit weight (FW), and fruit length (FL). A further QTL on chr09 also influenced ES, while five other QTLs affected FL. This study was the first to conduct genetic architecture analysis and QTL mapping in Chinese Hami melon with high-density markers and a large target population.

Download Full-text

Insights into the Genetic Architecture of Phenotypic Stability Traits in Winter Wheat

Agronomy ◽

10.3390/agronomy10030368 ◽

2020 ◽

Vol 10 (3) ◽

pp. 368 ◽

Cited By ~ 1

Author(s):

Dennis Lozada ◽

Arron Carter

Keyword(s):

Winter Wheat ◽

Pacific Northwest ◽

Genetic Architecture ◽

Heading Date ◽

Major Effect ◽

Snp Markers ◽

Genetic Loci ◽

Phenotypic Stability ◽

Trait Stability ◽

Genetic Complexity

Examining the architecture of traits through genomics is necessary to gain a better understanding of the genetic loci affecting important traits to facilitate improvement. Genomewide association study (GWAS) and genomic selection (GS) were implemented for grain yield, heading date, and plant height to gain insights into the genetic complexity of phenotypic stability of traits in a diverse population of US Pacific Northwest winter wheat. Analysis of variance using the Additive Main Effect and Multiplicative Interaction (AMMI) approach revealed significant genotype and genotype by environment interactions. GWAS identified 12 SNP markers distributed across 10 chromosomes affecting variation for both trait and phenotypic stability, indicating potential pleiotropic effects and signifying that similar genetic loci could be associated with different aspects of stability. The lack of stable and major effect loci affecting phenotypic variation supports the complexity of stability of traits. Accuracy of GS was low to moderate, between 0.14 and 0.66, indicating that phenotypic stability is under genetic control. The moderate to high correlation between trait and trait stability suggests the potential of simultaneous selection for trait and trait stability. Our results demonstrate the complex genetic architecture of trait stability and show the potential for improving stability in winter wheat using genomic-assisted approaches.

Download Full-text

Genetic Loci Associated with Resistance to Zucchini Yellow Mosaic Virus in Squash

Plants ◽

10.3390/plants10091935 ◽

2021 ◽

Vol 10 (9) ◽

pp. 1935

Author(s):

Swati Shrestha ◽

Vincent Njung’e Michael ◽

Yuqing Fu ◽

Geoffrey Meru

Keyword(s):

Mosaic Virus ◽

Bulked Segregant Analysis ◽

Zucchini Yellow Mosaic Virus ◽

Snp Markers ◽

Yellow Mosaic Virus ◽

Whole Genome ◽

Chromosome 2 ◽

Genetic Loci ◽

Single Nucleotide ◽

F2 Population

Zucchini Yellow Mosaic Virus (ZYMV) is an aphid-transmitted potyvirus that causes severe yield losses in squash (Cucurbita moschata) production worldwide. Development of resistant cultivars using traditional breeding approaches relies on rigorous and resource-intensive phenotypic assays. QTL-seq, a whole genome re-sequencing based bulked segregant analysis, is a powerful tool for mapping quantitative trait loci (QTL) in crop plants. In the current study, the QTL-seq approach was used to identify genetic loci associated with ZYMV resistance in an F2 population (n = 174) derived from a cross between Nigerian Local (resistant) and Butterbush (susceptible). Whole genome re-sequencing of the parents and bulks of resistant and susceptible F2 progeny revealed a mapping rate between 94.04% and 98.76%, and a final effective mapping depth ranging from 81.77 to 101.73 across samples. QTL-seq analysis identified four QTLs significantly (p < 0.05) associated with ZYMV resistance on chromosome 2 (QtlZYMV-C02), 4 (QtlZYMV-C04), 8 (QtlZYMV-C08) and 20 (QtlZYMV-C20). Seven markers within the QTL intervals were tested for association with ZYMV resistance in the entire F2 population. For QtlZYMV-C08, one single nucleotide polymorphism (SNP) marker (KASP-6) was found to be significantly (p < 0.05) associated with ZYMV resistance, while two SNPs (KASP-1 and KASP-3) and an indel (Indel-2) marker were linked to resistance within QtlZYMV-C20. KASP-3 and KASP-6 are non-synonymous SNPs leading to amino acid substitutions in candidate disease resistant gene homologs on chromosomes 20 (CmoCh20G003040.1) and 8 (CmoCh08G007140.1), respectively. Identification of QTL and SNP markers associated with ZYMV resistance will facilitate marker-assisted selection for ZYMV resistance in squash.

Download Full-text

Genetic architecture of schizophrenia: a review of major advancements

Psychological Medicine ◽

10.1017/s0033291720005334 ◽

2021 ◽

pp. 1-10

Author(s):

Sophie E. Legge ◽

Marcos L. Santoro ◽

Sathish Periyasamy ◽

Adeniran Okewole ◽

Arsalan Arsalan ◽

...

Keyword(s):

Genetic Architecture ◽

Association Studies ◽

Copy Number Variants ◽

Risk Scores ◽

Genome Wide Association Studies ◽

Loss Of Function ◽

Genetic Loci ◽

Significant Enrichment ◽

High Heritability ◽

Coding Variants

Abstract Schizophrenia is a severe psychiatric disorder with high heritability. Consortia efforts and technological advancements have led to a substantial increase in knowledge of the genetic architecture of schizophrenia over the past decade. In this article, we provide an overview of the current understanding of the genetics of schizophrenia, outline remaining challenges, and summarise future directions of research. World-wide collaborations have resulted in genome-wide association studies (GWAS) in over 56 000 schizophrenia cases and 78 000 controls, which identified 176 distinct genetic loci. The latest GWAS from the Psychiatric Genetics Consortium, available as a pre-print, indicates that 270 distinct common genetic loci have now been associated with schizophrenia. Polygenic risk scores can currently explain around 7.7% of the variance in schizophrenia case-control status. Rare variant studies have implicated eight rare copy-number variants, and an increased burden of loss-of-function variants in SETD1A, as increasing the risk of schizophrenia. The latest exome sequencing study, available as a pre-print, implicates a burden of rare coding variants in a further nine genes. Gene-set analyses have demonstrated significant enrichment of both common and rare genetic variants associated with schizophrenia in synaptic pathways. To address current challenges, future genetic studies of schizophrenia need increased sample sizes from more diverse populations. Continued expansion of international collaboration will likely identify new genetic regions, improve fine-mapping to identify causal variants, and increase our understanding of the biology and mechanisms of schizophrenia.

Download Full-text

Genetic Mechanisms Underlying Apimaysin and Maysin Synthesis and Corn Earworm Antibiosis in Maize (Zea mays L.)

Genetics ◽

10.1093/genetics/149.4.1997 ◽

1998 ◽

Vol 149 (4) ◽

pp. 1997-2006

Author(s):

E A Lee ◽

P F Byrne ◽

M D McMullen ◽

M E Snook ◽

B R Wiseman ◽

...

Keyword(s):

Helicoverpa Zea ◽

Larval Growth ◽

Corn Earworm ◽

Phenotypic Variance ◽

Significant Qtls ◽

F2 Population ◽

Genetic Mechanisms ◽

Trait Locus ◽

Maize Silks ◽

Related Compounds

Abstract C-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14.1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.

Download Full-text

Molecular Mapping of Loci Conferring Susceptibility to Spot Blotch and Resistance to Powdery Mildew in Barley Using the Sequencing-Based Genotyping Approach

Phytopathology ◽

10.1094/phyto-08-19-0292-r ◽

2020 ◽

Vol 110 (2) ◽

pp. 440-446 ◽

Cited By ~ 3

Author(s):

Yueqiang Leng ◽

Mingxia Zhao ◽

Jason Fiedler ◽

Antonín Dreiseitl ◽

Shiaoman Chao ◽

...

Keyword(s):

Powdery Mildew ◽

Molecular Mapping ◽

Recombinant Inbred Lines ◽

Major Gene ◽

Bipolaris Sorokiniana ◽

Spot Blotch ◽

Blumeria Graminis ◽

Seedling Stage ◽

Barley Cultivars ◽

Trait Locus

Spot blotch (SB) caused by Bipolaris sorokiniana and powdery mildew (PM) caused by Blumeria graminis f. sp. hordei are two important diseases of barley. To map genetic loci controlling susceptibility and resistance to these diseases, a mapping population consisting of 138 recombinant inbred lines (RILs) was developed from the cross between Bowman and ND5883. A genetic map was constructed for the population with 852 unique single nucleotide polymorphism markers generated by sequencing-based genotyping. Bowman and ND5883 showed distinct infection responses at the seedling stage to two isolates (ND90Pr and ND85F) of Bipolaris sorokiniana and one isolate (Race I) of Blumeria graminis f. sp. hordei. Genetic analysis of the RILs revealed that one major gene (Scs6) controls susceptibility to Bipolaris sorokiniana isolate ND90Pr, and another major gene (Mla8) confers resistance to Blumeria graminis f. sp. hordei isolate Race I, respectively. Scs6 was mapped on chromosome 1H of Bowman, as previously reported. Mla8 was also mapped to the short arm of 1H, which was tightly linked but not allelic to the Rcs6/Scs6 locus. Quantitative trait locus (QTL) analysis identified two QTLs, QSbs-1H-P1 and QSbs-7H-P1, responsible for susceptibility to spot blotch caused by Bipolaris sorokiniana isolate ND85F in ND5883, which are located on chromosome 1H and 7H, respectively. QSbs-7H-P1 was mapped to the same region as Rcs5, whereas QSbs-1H-P1 may represent a novel allele conferring seedling stage susceptibility to isolate ND85F. Identification and molecular mapping of the loci for SB susceptibility and PM resistance will facilitate development of barley cultivars with resistance to the diseases.

Download Full-text

PEMANFAATAN ASAP CAIR ALANG-ALANG (Imperata cylindrica) SEBAGAI PENGAWET TERHADAP KARAKTERISTIK BUAH PISANG MAKAU (Musa spp.)

AGROINTEK ◽

10.21107/agrointek.v12i1.3496 ◽

2018 ◽

Vol 12 (1) ◽

pp. 39

Author(s):

Dian Fitriarni ◽

Rafika Ayuni

Keyword(s):

Vitamin C ◽

Shelf Life ◽

Raw Materials ◽

Sugar Content ◽

Fruit Weight ◽

Imperata Cylindrica ◽

Alternative Methods ◽

Musa Spp ◽

Percentage Decrease ◽

Liquid Smoke

Research on the utilization of liquid smoke especially for preservation of fruit has been done and become one of alternative methods that can be used to maintain fruit shelf life. Liquid smoke raw materials can come from a variety of sources one of which comes from the Alang-alang (Imperata cylindrica). This study aims to determine the ability of liquid smoke made from alang-alang as a preservative of bananas and to know the effect on the characteristics of bananas. The sample used in this research is a local banana known as Pisang Makau (Musa spp). This research uses experimental method with 7 days of storage time. Initial stages of the research are cleaning the fruit, dyeing, drying, and storage at room temperature. This research uses liquid smoke from alang-alang by using 2 various concentrations 50% and 100%. The next stage is the analysis of the characteristics of bananas such as color, fruit texture, fruit weight, sugar content, and vitamin C levels. Based on the analysis results obtained by Pisang Makau with the treatment of liquid has a longer shelf life than the control. Based on the results of the analysis of the shelf life of fruit treated with liquid smoke decreased levels of sugar and vitamin C levels. Percentage decrease levels of sugar and vitamin C between the fruit with the treatment and control not much different. This shows that liquid smoke from alang-alang has the ability to retain the shelf life of bananas without affecting sugar and vitamin C levels in bananas in this case for Pisang Makau. Levels of sugar and vitamin C in bananas decreased during the process of storage and bunding of fruit

Download Full-text

Variability components and heritability of pomological and chemical characteristics in sour cherry clones of cultivar Montmorency

Genetika ◽

10.2298/gensr0703297f ◽

2007 ◽

Vol 39 (3) ◽

pp. 297-304 ◽

Cited By ~ 2

Author(s):

Milica Fotiric ◽

Dragan Nikolic ◽

Vera Rakonjac

Keyword(s):

Acid Content ◽

Sugar Content ◽

Sour Cherry ◽

Fruit Weight ◽

Solid Content ◽

Stem Length ◽

Soluble Solid Content ◽

Chemical Characteristics ◽

Total Acid ◽

Fruit Length

In 12 sour cherry clones of cultivar Montmorency 5 pomological (fruit length, fruit width, fruit weight, stone weight and fruit stem length) and 4 chemical characteristics (soluble solid content, total acid content, invert sugar content and total sugar content) were investigated. Based on results of analysis of variance for all examined characteristics, variability components, coefficients of genetic and phenotypic variation and coefficient of heritability in a broader sense were calculated. Considering components of total variability, year represented the component that caused variability of majority examined characteristics in the highest percentage. Coefficients of genetic variation showed that in investigated clones total acid content varied the least (CVg = 1.79%), and the most fruit weight (CVg = 11.41%). The lowest phenotypic varying was determined for fruit length (CVf = 4.01%) but the highest for fruit weight (CVf = 13.86%). Coefficient of heritability was the highest for stone weight (h2 = 70.27%), and the lowest for total acid content (h2 = 7.73%).

Download Full-text

Analysis of pomological traits in new promising sweet cherry genotypes

Genetika ◽

10.2298/gensr1303873a ◽

2013 ◽

Vol 45 (3) ◽

pp. 873-880 ◽

Cited By ~ 5

Author(s):

Milica Fotiric-Aksic ◽

Tihomir Nikolic

Keyword(s):

Sweet Cherry ◽

Sugar Content ◽

Fruit Size ◽

Fruit Weight ◽

Solid Content ◽

Soluble Solid Content ◽

Fresh Market ◽

Total Sugar Content ◽

Ripening Time ◽

Chemical Content

Sweet cherry breeding programs are interested in developing new cultivars that are very early or very late in ripening, high yielding, with excellent fruit size and quality. The aim of this study was to evaluate new, promising, sweet cherry genotypes (G-1 and G-2) for ripening time, fruit morphology and fruit chemical content, and compare it with the standard sweet cherry cultivars (Bigarreau Jaboulay, B. H. Burlat, Seneca, Hedelfiger Riesenkirsche, Germersdorfer Grosse Kirsche, Emperor Francis and Bing). Experiment was done during four consecutive years (2006-2009) in Grocka, near Belgrade. The earliest fruit ripening was recorded in G-2 (22nd April) while the latest in `Bing` (2nd June). Fruit weight varied from 5.83 g (G-2) up to 8.93 g (G-1). Soluble solid content and total sugar content were the lowest in genotype G-2 (10.48%; 8.45%, respectively) but the highest in Emperor Francis (18.28%; 15.98%, respectively). No matter the fact that some standard cultivars showed better results for some traits, genotypes G-1 and G-2 are considered very promising. So, genotype G-1 could be intended for table consumption since it ripens 2-3 days after cv. B. H. Burlat, but have much higher fruit weight. Also, genotype G-2, the earliest in this trial, showed satisfactory fruit weight for this ripening time, which makes it very interesting for fresh market production.

Download Full-text

STIMULASI HASIL MELON ( Cucumis melo, L) DENGAN MENGGUNAKAN BIOTO GROW GOLD (BGG)

Jurnal Ilmiah Pertanian ◽

10.31849/jip.v15i1.1481 ◽

2018 ◽

Vol 15 (1) ◽

pp. 35-41

Author(s):

SAHINDAH ARITONANG ◽

SURTINAH SURTINAH

Keyword(s):

Data Analysis ◽

Cucumis Melo ◽

Sugar Content ◽

Fruit Weight ◽

Leaf Length ◽

Stem Diameter ◽

Leaf Width ◽

Randomized Design ◽

Cucumis Melo L ◽

Melon Fruit

The experiment was conducted experimentally using non-factorial Randomized Design (RAL) with 5 (five) treatment levels without Bioto Grow Gold, Bioto Grow Gold 1 ml liter-1 water, Bioto Grow Gold 2 ml liter -1 water, giving Bioto Grow Gold 3 ml liter-1 water and giving Bioto Grow Gold 4 ml liter-1 water. The data analysis used variance and continued with a different test of Duncan treatment average at p 0.05. The results showed that BGG treatment had the significant effect on leaf length, leaf width, stem diameter, flowering age, fruit circumference, fruit weight, a thickness of flesh and sugar content of melon fruit. The best treatment is giving Bioto Grow Gold 3 ml liter-1 water.

Download Full-text

Mapping of Resistance Genes to Brown Planthopper in Untup Rajab, an Indonesian Local Rice Variety

Jurnal AgroBiogen ◽

10.21082/jbio.v14n2.2018.p75-84 ◽

2018 ◽

Vol 14 (2) ◽

pp. 75

Author(s):

Muhamad Yunus ◽

Diani Damayanti ◽

Ahmad Dadang ◽

Ahmad Warsun ◽

Dani Satyawan ◽

...

Keyword(s):

Resistance Genes ◽

Quantitative Resistance ◽

Insect Pest ◽

Rice Variety ◽

Brown Planthopper ◽

Snp Markers ◽

Chromosome 8 ◽

F2 Population ◽

Resistant Varieties ◽

Test Population

Brown planthopper (BPH) is a major rice pest in Indonesia. The most economical and effective approach to control the insect pest is by using resistant varieties. Exploring for resistance genes is, therefore, a prerequisite for effective breeding program for BPH resistance. This study aimed to map BPH resistance genes in Untup Rajab, an Indonesian local rice variety. Genetic map was constructed using an F2 population from a cross between TN-1 and Untup Rajab, and SNP markers from RiceLD SNP Chip. Phenotyping was performed using bulk seedling test on F2:3 seedlings against two BPH populations, i.e. X1 and S1. Four QTLs were identified on chromosomes 5, 6, 8, and 11 with PVE values of 7.63%, 9.40%, 17.66%, and 3.05%, respectively. Relatively normal distribution of resistance phenotype and the relatively low PVE values indicate that Untup Rajab has a quantitative resistance to BPH with two different resistance loci identified for each BPH test population. The QTL on chromosome 8 overlaps with OsHI-LOX gene, which is associated with resistance to BPH, and adjacent to another QTL for resistance to green leafhopper. The QTL on chromosome 6 was found near OsPLDα4 and OsPLDα5 genes which are related to BPH resistance. Meanwhile, the QTL intervals on chromosome 5 and 11 did not overlap with any known BPH QTLs or genes, which make them attractive candidates for novel BPH resistance gene discovery.

Download Full-text