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.     

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.     

Reaction of <Emphasis Type="Italic">Phaseolus</Emphasis> spp. genotypes to ashy stem blight caused by <Emphasis Type="Italic">Macrophomina phaseolina</Emphasis>

Ashy stem blight (ASB) caused by Macrophomina phaseolina (Tassi) Goidanich (Mp) is a devastating seed-transmitted disease in common bean in the tropics. The identification of resistant cultivars throughout the cropping season contributes to disease management. Resistance is found in the primary and tertiary gene pools. Our objectives were to determine (1) the reaction of Phaseolus spp. genotypes to two Mp isolates at vegetative and reproductive stages, (2) the area under disease progress curve (AUDPC), and (3) resistant plants per genotype at harvest. Twenty-three genotypes from different origins were planted in the greenhouse in 2016 and 2017. One less-aggressive Mp (PRJD16) and one more-aggressive (PRI16) isolate were inoculated one and three times, respectively, by the cut-stem method. ‘Beníquez’, ‘Othello’, and ‘Verano’ were highly susceptible (mean scores >8.0, and AUDPC values from 264.6 to 300.8) to both isolates. BAT 477 and NY6020-4 were intermediate (5.6 and 6.2; AUDPC: 161.6 and 187.1) to PRJD16 and susceptible (7.4 and 8.2; AUDPC: 209.4 and 235.1) to PRI16. Resistant genotypes (mean scores ≤3) were not identified in this study. However, A 195, ‘Badillo’, and ‘PC 50’ possessed lower mean scores (4.3–5.4) and AUDPC values (126.4–150.9) to both isolates. Furthermore, A 195 had the highest percentage of resistant plants (55.6%) followed by PC 50, I9365-31, and PI 321637 (27.8%) to PRJD16 at harvest. Thus, the identification of resistant parents across Phaseolus species is necessary to increase the levels of ASB resistance in common bean cultivars throughout the entire cropping season.     

Tall fescue forage mass in a grass-legume mixture: predicted efficiency of indirect selection

High fertilizer prices and improved environmental stewardship have increased interest in grass-legume mixed pastures. It has been hypothesized, but not validated, that the ecological combining ability between grasses and legumes can be improved by breeding specifically for mixture performance. This experiment examined the predicted efficiency of selection in a grass monoculture environment to indirectly improve tall fescue (Lolium arundinaceum (Schreb.) Darbysh.) forage mass in a grass-legume mixture. Heritability, genetic and rank correlations, and selection efficiencies were estimated for forage mass in a tall fescue half-sib population grown as spaced-plants overseeded with either turf-type tall fescue (monoculture) or alfalfa (mixture). Heritability for tall fescue forage mass in monoculture ranged from 0.32 to 0.70 and were always similar or greater than those in mixture (range 0.27–0.55) for four successive harvests and annual total. Genetic correlations between monoculture and mixture tall fescue forage mass varied with values of 0.48, 0.92, ?0.31, 0.70, and 0.25 in June, July, August, October, and annual total, respectively. Indirect selection efficiencies exceeded or approached direct selection for mixtures only in July and October (1.29, and 0.73, respectively). Whereas, indirect selection efficiencies were low in June, August, and annual forage mass (0.58, ?0.31, and 0.28, respectively). Moreover, low Spearman’s rank correlations (?0.03 to 0.35) indicated differing half-sib family performance between the monoculture and mixture environments. Results indicate that direct selection should be used to improve tall fescue forage mass in a grass-legume mixture, and support the hypothesis of increasing ecological combining ability by breeding for mixtures per se.