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.     

Estimating gene action,combining ability and heterosis for grain yield and agronomic traits in extra-early maturing yellow maize single-crosses under three agro-ecologies of Ghana

Maize (Zea mays L.) is the most important cereal crop produced in Ghana. However, yield of the crop is generally low, producing just about 1.7 t/ha. The low yield is attributed to continuous use of local/unimproved varieties. Generally, hybrid varieties have proven to out-yield the local/unimproved varieties due to improved vigour. Development of hybrid varieties depend on good understanding of combining ability and inheritance of important quantitative traits such as grain yield (GY). 45 half-diallel crosses generated from 10 extra-early maturing yellow inbred lines were evaluated in 2015 under rain-fed conditions. The objectives were to determine the genetic control, breeding value and estimate heritability for GY and agronomic traits of the inbred lines under contrasting growing environments in Ghana. General combining ability (GCA) and specific combining ability (SCA) were important in the inheritance of GY and agronomic traits of the inbred lines. However, GCA was more important than SCA across environments to suggest that additive gene action was more important than non-additive gene action in the inheritance of GY and agronomic traits in the inbred lines. High broad-sense heritability, for GY and other agronomic traits indicated preponderance of additive gene action in trait expression, thus, selection based on phenotypic expression could be feasible. Inbred lines P1, P4 and P8 were good combiners for high GY. The genotype, P4 × P8, was identified as the ideal and most yielding single-cross hybrid across research environments and should be further tested on-farm before commercialization.     

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.     

QTL mapping and analysis of epistatic interactions for grain yield and yield-related traits in <Emphasis Type="Italic">Triticum turgidum</Emphasis> L. var. <Emphasis Type="Italic">durum</Emphasis>

A quantitative trait loci (QTL) analysis of grain yield and yield-related traits was performed on 93 durum wheat recombinant inbred lines derived from the cross UC1113 × Kofa. The mapping population and parental lines were analyzed considering 19 traits assessed in different Argentine environments, namely grain yield, heading date, flowering time, plant height, biomass per plant, and spikelet number per ear, among others. A total of 224 QTL with logarithm of odds ratio (LOD) ≥ 3 and 47 additional QTL with LOD > 2.0 were detected. These QTL were clustered in 35 regions with overlapping QTL, and 12 genomic regions were associated with only one phenotypic trait. The regions with the highest number of multi-trait and stable QTL were 3BS.1, 3BS.2, 2BS.1, 1BL.1, 3AL.1, 1AS, and 4AL.3. The effects of epistatic QTL and QTL × environment interactions were also analyzed. QTL putatively located at major gene loci (Rht, Vrn, Eps, and Ppd) as well as additional major/minor QTL involved in the complex genetic basis of yield-related traits expressed in Argentine environments were identified. Interestingly, the 3AL.1 region was found to increase yield without altering grain quality or crop phenology.     

Heritability of the resistance to pepper huasteco yellow vein virus in wild genotypes of <Emphasis Type="Italic">Capsicum annuum</Emphasis>

Pepper huasteco yellow vein virus (PHYVV) is the main virus of pepper crop in Mexico. No resistant cultivars are available and resistance breeding is hampered by the lack of knowledge of heritability (h ²) of PHYVV resistance. This is a continuation of previous studies and the objectives were to analyze the h ² and the behavior of the resistant trait to PHYVV. Four resistant assays were done with three resistant wild lines (UAS12, UAS13 and UAS10) of Capsicum annuum in the S4, S5, S6 and S7 generation under greenhouse conditions. Plants from all tests were inoculated with PHYVV through Bemisia tabaci. Line UAS12 was the most resistant showing a significantly proportion of resistant plants, less disease symptoms and longer incubation time, followed by the lines UAS13 and UAS10 in all assays. Distribution of symptoms showed a bimodal tendency in all the trials, suggesting that two groups of genes are involved in this resistance trait. The lines UAS12, UAS13 and UAS10 showed the same pattern of response to selection with an average of h ² of 0.17, 0.06, 0.02 and 0.00 in the S4, S5, S6 and S7, respectively. These results indicate that all lines responded positively to the selection in the S4, S5 and S6, whereas in the S7 there was no response by the possible exhaustion of variation. Line UAS12 is the most promising genotype and the lines UAS13 and UAS10 are genetic resources that can be supplemented to breed the resistance of PHYVV. These results provides basic information for resistance breeding.     

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.