Identification of favorable alleles in the <Emphasis Type="Italic">non</Emphasis>-<Emphasis Type="Italic">yellow coloring 1</Emphasis> gene by association mapping in maize

Association mapping was conducted to explore favorable alleles of the chlorophyll-related non-yellow coloring 1 (NYC1) gene under light and dark using an association panel of 146 maize inbred lines. A total of 14 polymorphic sites were identified to be significantly associated with at least one of the chlorophyll-related traits at the seedling stage. Four single nucleotide polymorphisms (SNPs) (S320, S2951, S3901, and S3355) from the NYC1 gene were respectively strongly associated with chlorophyll b (chlb), the ratio of chlorophyll a to chlorophyll b (chl_ratio), chlorophyll a degradation (chla_deg), and total chlorophyll degradation (total_chl_deg). SNPs S320 (C/A) in exon 1, and S2951 (A/G) in intron 8 was related to chlb, with 6.01 and 8.89% of phenotypic variation under light treatment, respectively. Under dark treatment, SNP S3901 (C/T), located in 3′ untranslated region (3′UTR), was associated with chl_ratio, explaining 7.01% of the observed phenotypic variation, whereas SNP S3355 (C/G) in intron 9 explained 6.48 and 5.18% of phenotypic variations in chla_deg and total_chl_deg, respectively. Taken together, these results indicated that the NYC1 gene plays an important role in chlorophyll content and other related traits, and different sites act on chlorophyll metabolism under different light intensities in maize seedlings. Furthermore, these findings improve our understanding of the genetic basis of chlorophyll metabolism under different light conditions.     

Development of male-specific markers and identification of sex reversal mutants in papaya

Papaya is a productive and nutritious fruit grown in tropical and sub-tropical regions worldwide. It is polygamous with three sex types: female, male and hermaphrodite. Sex determination in papaya is controlled by an XY sex chromosome system with two slightly different Y chromosomes, Y for males and Y^h for hermaphrodites. Comparative analysis of the hermaphrodite-specific region of Y^h chromosome (HSY) and male-specific region of Y chromosome (MSY) revealed 99.6% sequence identity, which explains why DNA markers that amplify for both males and hermaphrodites have easily been developed, but not for the male trait specifically. We examined the 0.4% sequence differences, and found 1887 indels and 21,088 SNPs between MSY and HSY. The vast majority of indels are single nucleotide or few base pairs. A large male-specific retrotransposon insertion of 8396 bp was used to develop two papaya male-specific markers, PMSM1 and PMSM2 that amplify 585 and 548 bp fragments, respectively. These two markers were tested in 11 gynodioecious and four dioecious varieties along with autosomal DNA marker 71E and male/hermaphrodite marker W11, and the results showed clear separation of male from hermaphrodite and female. PMSM1 and PMSM2 were also used to test the sex type of six sex male-to-hermaphrodite reversal mutants which are crucial materials for validating candidate genes for sex determination in papaya. Our result showed all six mutants were positive for the male-specific markers. These male-specific markers can be used to distinguish gynodioecious and dioecious cultivars in papaya seed market, and facilitate genetic and genomic research for papaya improvement.     

Polymorphisms of the <Emphasis Type="Italic">FT</Emphasis> gene as a tool to identify underground rhizome types of bamboos

The Flowering Locus T (FT)-like genes of angiosperms are highly conserved. The FT-encoded proteins include a phosphatidylethanolamine-binding domain that is involved in the control of the shoot apical meristem identity and flowering time. In the present study, FT genes were investigated in 20 bamboo species that are grouped into sympodial, mixed and scattered bamboos based on their morphology. All examined orthologous FT genes consisted of four exons and three introns. Their encoded protein sequences contained the critical amino acid residues Tyr85, Glu109, Leu128, Tyr134, Trp138, Arg139, Gln140 and Asn152, of which each possesses a biological function. The DNA sequences were rich in single nucleotide polymorphism (SNP) sites. The SNP frequency was 1 SNP/16.8 bp, and the nucleotide diversity (π) equaled 0.265. Some SNPs altered restriction enzyme sites or resulted in changes in amino acid contents. The correlation analysis showed that several SNPs were informative in relation to the underground rhizome types of bamboos. Therefore, FT polymorphisms could be used as a tool to identify the underground rhizome types of bamboos. The phylogenetic tree constructed based on the FT gene sequences showed that the obtained clustering was consistent with the underground rhizome types. The SNP markers developed in the present study will provide information on the genetic diversity of bamboos and they can aid taxonomic study as well.     

Development and application of a molecular marker for TMV resistance based on <Emphasis Type="Italic">N</Emphasis> gene in tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis>)

Tobacco mosaic virus (TMV) caused serious loss in yield and quality of tobacco every year. It is a long-term goal to improve the tobacco resistance against TMV by tobacco breeding. N gene was the firstly reported TMV-resistant gene, which showed resistance against all Tobamoviruses except the Ob stain and belonged to the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant resistance (R) genes. At present, N gene had already been widely used in tobacco conventional breeding, but there is rare available molecular maker used in marker-assisted selection of TMV resistance. In this study, we designed a pair of primers that specific amplify N gene fragment based on the sequence of N gene intron III, named N-marker. Then, we identified TMV resistance by two selecting methods, PCR with N-marker and inoculated with the TMV-C strain. Results from the two method showed that (1) 13 varieties among 67 tobacco varieties displayed hypersensitive reaction when inoculated with the TMV-C strain, also contained N gene fragments screened by PCR with N-marker; (2) 105 strains of 200 BC1 strains showed resistance against TMV when inoculated with TMV-C strain, meanwhile, 103 of the 105 strains contained N gene fragment verified by PCR with N-marker. Therefore, the N-marker is reliable for high throughput screening of germplasm resources and tobacco breeding materials in selection of N-mediated TMV resistance. Our study not only developed a molecular marker for tobacco breeding, but also identified new germplasm resources that are resistant to TMV.     

The delay of flowering time in almond: a review of the combined effect of adaptation,mutation and breeding

Regulation of flowering time in almond, as in other Prunus species, is a complex process involving both chill and heat requirements. Following exposure to appropriate consecutive periods of cold and warm temperatures, the buds break dormancy and sprout or flower depending on bud type. To maximize flowering and subsequent vegetative growth and fruit set, chilling and ensuing warm temperature requirements have to be fully satisfied. Because of its potential for very early flowering, flowering time in almond is a major determinant of its adaptation to new environments. In colder regions, Late-flowering is often necessary to avoid frost damage during and just after flowering. Consequently, the selection of delayed flowering times remains an important objective in almond improvement programs. Flowering time is considered a quantitative though highly heritable trait. In addition, a dominant gene (Late flowering, Lb), originally identified in a spontaneous mutation of the Californian almond cultivar ‘Nonpareil’, was also described. The objective of this review is a comparative analysis of the effects of regional adaptation, breeding and mutation on the delay of flowering time in new almond cultivars. Findings indicate that the adaptation of almonds from the Mediterranean basin to colder regions in Northern Europe and America has been mainly achieved through delayed flowering. These adapted late-flowering cultivars have usually been developed by selecting desired quantitative genes within each regional germplasm. Additional progress thus appears achievable with a more comprehensive understanding of the quantitative and qualitative genetics controlling this trait. The use of molecular markers for the early selection of genes conferring late flowering, including both spontaneous mutations as well as unique regional germplasm, should allow development of even later cultivars including ultra-late cultivars flowering as into April.     

Using unsupervised learning techniques to assess interactions among complex traits in soybeans

Soybean yield components and agronomic traits are connected through physiological pathways that impose tradeoffs through genetic and environmental constraints. Our primary aim is to assess the interdependence of soybean traits by using unsupervised machine learning techniques to divide phenotypic associations into environmental and genetic associations. This study was performed on large scale, jointly analyzing 14 quantitative traits in a large multi-parental population designed for genetic studies. We collected phenotypes from 2012 to 2015 from a soybean nested association panel with 40 families of approximately 140 individuals each. Pearson and Spearman correlations measured phenotypic associations. A multivariate mixed linear model provided genotypic and environmental correlations. To evaluate relationships among traits, the study used principal component and undirected graphical models from phenotypic, genotypic, and environmental correlation matrices. Results indicate that high phenotypic correlation occurs when traits display both genetic and environmental correlations. In genetic terms, length of reproductive period, node number, and canopy coverage play important roles in determining yield potential. Optimal grain yield production occurs when the growing environment favors faster canopy closure and extended reproductive length. Environmental associations found among yield components give insight into the nature of yield component compensation. The use of unsupervised learning methods provides a good framework for investigating interactions among various quantitative traits and defining target traits for breeding.     

Improved genetic parameter estimations in zoysiagrass by implementing post hoc blocking

Randomized complete block (RCB) design is the most widely used experimental design in biological sciences. As number of treatments increases, the block size become larger and it looses the capacity to control the variance within block, which is its original purpose. A method known as post hoc blocking could be used in these cases to improve the genetic parameter estimation and thus obtain an unbiased assessment of the performance of a given treatment. In trufgrass breeding, as other breeding program, this is a common challenge. The goal of this study was to test the capacity of different post hoc blocking designs to improve the genetic parameter estimation of zoysiagrass (Zoysia spp.). We evaluated two post hoc blocking designs; row–column (R–C) and incomplete block (IB) designs on five genotype trials located in Florida. The results showed that post hoc R–C design had superior model fitting than both the original RCB and the post hoc IB designs when studied at the single measurement level and at the site level. The narrow-sense heritability (0.24–0.40) and the genotype-by-measurement correlation (0.57–0.99) did not change significantly when R–C was compared to the original RCB design. The ranking of the top performing genotypes changed considerably when comparing RCB to R–C design, but the degree depended on the location analyzed. We conclude that the change in the ranking of the top (potentially select individuals) is coming from the better control of intra-block environmental variation, and this could potentially have a significant impact on the breeding selection process.     

Determining resistance to <Emphasis Type="Italic">Fusarium verticillioides</Emphasis> and fumonisin accumulation in African maize inbred lines resistant to <Emphasis Type="Italic">Aspergillus flavus</Emphasis> and aflatoxins

Fusarium verticillioides and Aspergillus flavus cause Fusarium ear rot (FER) and Aspergillus ear rot (AER) of maize, respectively. Both pathogens are of concern to producers as they reduce grain yield and affect quality. F. verticillioides and A. flavus also contaminate maize grain with the mycotoxins fumonisins and aflatoxins, respectively, which has been associated with mycotoxicosis in humans and animals. The occurrence of common resistance mechanisms to FER and AER has been reported. Hence, ten Kenyan inbred lines resistant to AER and aflatoxin accumulation were evaluated for resistance to FER, F. verticillioides colonisation and fumonisin accumulation; and compared to nine South African lines resistant to FER and fumonisin accumulation. Field trials were conducted at three localities in South Africa and two localities in Kenya. FER severity was determined by visual assessment, while F. verticillioides colonisation and fumonisin content were quantified by real-time PCR and liquid chromatography tandem mass spectrometry, respectively. Significant genotype x environment interactions was determined at each location (P ≤ 0.05). Kenyan inbred CML495 was most resistant to FER and F. verticillioides colonisation, and accumulated the lowest concentration of fumonisins across localities. It was, however, not significantly more resistant than Kenyan lines CML264 and CKL05015, and the South African line RO549 W, which also exhibited low FER severity (≤5%), fungal target DNA (≤0.025 ng μL^?1) and fumonisin levels (≤2.5 mg kg^?1). Inbred lines resistant to AER and aflatoxin accumulation appear to be promising sources of resistance to F. verticillioides and fumonisin contamination.