Modern Commercial Cultivars Research Articles

The release of ‘LCP 85‐384’ and its contribution to the Louisiana sugar industry

AbstractBasic breeding efforts initiated at the USDA‐ARS in Houma, LA, in the late 1950s allowed Louisiana sugarcane breeders, once again, to cross with the wild germplasm of cultivated sugarcane, Sacharum spontaneum. ‘LCP 85‐384’ was the first success story from this effort and was quickly adopted by growers. It became clear that the cultivar would prove to be substantially impactful to the Louisiana sugar industry. Performing at unprecedented yields in ratoon crops, LCP 85‐384 changed how Louisiana growers would manage their crops. The variety proved to possess traits that fared well in the subtropical production zones of the state. Substantial stalk populations seemed to play a vital role in the necessary ratoon ability and consequent cold tolerance necessary for production in Louisiana. After significant disease pressure, the variety quickly declined in production acreage, but not in impact. It continued to provide sustained progress as a parent for years, contributing to most modern commercial cultivars in Louisiana. Today, LCP 85‐384 and its progeny are used in breeding and genetic research to usher in the next era of progress in the Louisiana sugar industry. Meanwhile, through cooperative efforts of breeding programs around the world, it is making its mark on the sugarcane industries of Argentina in much the same way as it did in Louisiana. In the future, it is expected that the progress made in the breeding program will continue by building upon the gains achieved from LCP 85‐384 and its progeny for the sustained success of the Louisiana sugarcane industry.

Development and molecular cytogenetic identification of a new wheat-rye 6RL ditelosomic addition and 1R (1B) substitution line with powdery mildew resistance

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious disease that critically threatens the yield and quality of wheat (Triticum aestivum L.). Using effective powdery mildew resistance genes is considered to be the optimal choice for controlling this disease. Against the background of high homogeneity among the modern commercial cultivars that are mainly derived from conventional interbreeding, the resistance genes from wheat relatives have especially prominent advantages. Octoploid triticale, produced by common wheat and rye (Secale cereale L.) through distant hybridization, is a new synthetic species and valuable gene donor for wheat improvement. In this study, we developed a wheat-rye line YT5 through the hybridization of octoploid triticale and two wheat lines. YT5 was confirmed to be a 6RL ditelosomic addition and 1R (1B) substitution line using genomic in situ hybridization (GISH), multicolor fluorescence in situ hybridization (mc-FISH), multicolor GISH (mc-GISH) and molecular marker analysis. Genetic analysis showed that the powdery mildew resistance in YT5 was derived from the rye chromosome arm 6RL. After inoculation with different Bgt isolates at the seedling stage, YT5 had compound reaction patterns with both obvious spores and hypersensitivity and gradually became highly resistant until the adult-plant stage, thus showing a resistance response significantly different from the reported Pm genes from rye chromosome 6RL. Meanwhile, YT5 showed promising agronomic performance and hence is expected to be an elite resistance donor for wheat improvement. To promote the transfer of the chromosome arm 6RL of YT5 in marker-assisted selection breeding, we selected and verified two 6RL-specific kompetitive allele-specific PCR markers that can be applied to efficiently detect this chromosome arm in different wheat backgrounds.

Novel Sources of Resistance to Stagonospora nodorum and Role of Effector-Susceptibility Gene Interactions in Wheat of Russian Breeding

Virulence factors of the pathogen Stagonospora nodorum Berk. are numerous necrotrophic effectors (NEs) (SnTox), which interact with the products of host susceptibility genes (Snn), causing the development of the disease. In this study, 55 accessions of bread spring and winter wheat were screened for sensitivity to NEs SnToxA, SnTox1, and SnTox3 using different isolates of S. nodorum. In the studied panel of wheat, 47 accessions were modern commercial cultivars grown in Russia and 8 cultivars were historic wheat accessions from the N. I. Vavilov Institute of Plant Genetic Resources in Russia. In general, our wheat panel differed from other wheat collections with available data in that it was less sensitive to SnToxA and SnTox3, and more sensitive to SnTox1. Six sources of strong SNB resistance were identified in our wheat panel. In addition, during the study, wheat cultivars were identified as appropriate objects in which to study the different effects of SnTox-Snn interactions, which is important for marker-assisted selection for SNB resistance. The current study has shown, for the first time, that the expression level of Snn1 and Tsn1 susceptibility genes and the disease severity of the different wheat cultivars are interconnected. Future work should focus on the deep characterization of SnTox-Snn interactions at the molecular level.

A draft chromosome-scale genome assembly of a commercial sugarcane

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum, S. spontaneum, and several other Saccharum species, resulting in an auto-allopolyploid with 8–12 copies of each chromosome. The current genome assembly gold standard is to generate a long read assembly followed by chromatin conformation capture sequencing to scaffold. We used the PacBio RSII and chromatin conformation capture sequencing to sequence and assemble the genome of a South East Asian commercial sugarcane cultivar, known as Khon Kaen 3. The Khon Kaen 3 genome assembled into 104,477 contigs totalling 7 Gb, which scaffolded into 56 pseudochromosomes containing 5.2 Gb of sequence. Genome annotation produced 242,406 genes from 30,927 orthogroups. Aligning the Khon Kaen 3 genome sequence to S. officinarum and S. spontaneum revealed a high level of apparent recombination, indicating a chimeric assembly. This assembly error is explained by high nucleotide identity between S. officinarum and S. spontaneum, where 91.8% of S. spontaneum aligns to S. officinarum at 94% identity. Thus, the subgenomes of commercial sugarcane are so similar that using short reads to correct long PacBio reads produced chimeric long reads. Future attempts to sequence sugarcane must take this information into account.

Incidence, Geographical Distribution, and Genetic Diversity of Sugarcane Striate Virus in Saccharum Species in China.

A novel virus of the genus Mastrevirus, family Geminivirdae, has been reported in sugarcane germplasm collections in Florida, Guadeloupe, and Réunion, and was named sugarcane striate virus (SStrV). Although the full-length sequence of an SStrV isolate from China was obtained in 2015, the incidence, geographical distribution, and genetic diversity of this virus remained unclear. A single leaf sample from 2,368 sugarcane plants from main sugarcane-producing regions of China and germplasm collections were tested for SStrV by PCR. Average virus incidence was 25.1% for field-collected samples, and SStrV was detected in most Saccharum species and two sugarcane-related species, with the highest incidence in Saccharum officinarum (44.1%) followed by Saccharum spp. local varieties (33.3%) grown for chewing cane for a long time. The virus incidence was much lower (6.8%) in modern commercial cultivars (Saccharum spp. hybrids). Phylogenetic trees based on full-length genomes of 157 SStrV isolates revealed that Chinese isolates comprised strains A and B, but not C and D, that were reported in Florida, U.S.A. SStrV strain A was the most prominent (98.7%) and widespread strain in China and was further divided into eight subgroups. Almost half (45.6%) of the SStrV-positive samples from S. officinarum and Saccharum spp. local varieties were coinfected with sugarcane mosaic disease viruses or sugarcane yellow leaf virus. Interestingly, most of the plants infected by strain A of SStrV were asymptomatic. SStrV appears to be widespread in China, and its influence on chewing cane deserves further investigation.

Tomato Domestication Attenuated Responsiveness to a Beneficial Soil Microbe for Plant Growth Promotion and Induction of Systemic Resistance to Foliar Pathogens.

Crop domestication events followed by targeted breeding practices have been pivotal for improvement of desirable traits and to adapt cultivars to local environments. Domestication also resulted in a strong reduction in genetic diversity among modern cultivars compared to their wild relatives, though the effect this could have on tripartite relationships between plants, belowground beneficial microbes and aboveground pathogens remains undetermined. We quantified plant growth performance, basal resistance and induced systemic resistance (ISR) by Trichoderma harzianum, a beneficial soil microbe against Botrytis cinerea, a necrotrophic fungus and Phytophthora infestans, a hemi-biotrophic oomycete, in 25 diverse tomato genotypes. Wild tomato related species, tomato landraces and modern commercial cultivars that were conventionally or organically bred, together, representing a domestication gradient were evaluated. Relationships between basal and ISR, plant physiological status and phenolic compounds were quantified to identify potential mechanisms. Trichoderma enhanced shoot and root biomass and ISR to both pathogens in a genotype specific manner. Moreover, improvements in plant performance in response to Trichoderma gradually decreased along the domestication gradient. Wild relatives and landraces were more responsive to Trichoderma, resulting in greater suppression of foliar pathogens than modern cultivars. Photosynthetic rate and stomatal conductance of some tomato genotypes were improved by Trichoderma treatment whereas leaf nitrogen status of the majority of tomato genotypes were not altered. There was a negative relationship between basal resistance and induced resistance for both diseases, and a positive correlation between Trichoderma-ISR to B. cinerea and enhanced total flavonoid contents. These findings suggest that domestication and breeding practices have altered plant responsiveness to beneficial soil microbes. Further studies are needed to decipher the molecular mechanisms underlying the differential promotion of plant growth and resistance among genotypes, and identify molecular markers to integrate selection for responsiveness into future breeding programs.

Genetic Diversity of Old and Local Apple (Malus × domestica Borkh.) Cultivars from the Collection of VIR according to AFLP Analysis

The genetic diversity of 123 apple accessions from the collection of the research and production base Pushkin and Pavlovsk Laboratories of VIR, including landraces, Soviet cultivars, and commercial Russian and foreign cultivars, was for the first time estimated using the AFLP technique. A total of 355 fragments were obtained, 319 of which were polymorphic (89.86%), and each of the accessions had a unique set of AFLP fragments. The level of diversity of modern commercial cultivars was lower (74.11%, Не = 0.202, I = 0.302) as compared with landraces (89.20%, Не = 0.238, I = 0.366). A wide range of genetic differences between the studied accessions (0.99–0.63) was demonstrated. The statistical analysis of the data obtained made it possible to divide the studied samples into two groups. The first group included most of the analyzed landraces; with no clear differentiation of these landraces by origin. The second group included modern commercial Russian and foreign apple cultivars, Soviet cultivars, and some landraces.

Agronomic Performance of Brassicaceae Oilseeds in Multiple Environments Across the Western USA

Brassicaceae oilseed crops can provide rotation benefits to dryland wheat (Triticum aestivum L.) and supply feedstock for biofuel production. However, growers face decisions about what oilseed crop is best suited for an environment. The objective of this study was to determine how varying production environments affect the agronomic performance of modern cultivars of six Brassicaceae crop species and identify ideal genotypes for seven growing environments spanning four ecoregions. A field experiment was replicated in Colorado, Idaho, Iowa, Minnesota, Montana, North Dakota, and Oregon, USA, between 2013 and 2016 to measure seed and oil yields of seed for four cultivars of Brassica napus, two of B. carinata, two of B. juncea, two of Sinapis alba, one of B. rapa, and one of Camelina sativa. Also, δ13C signature of seed was used as an indicator of water limitation. Generally, across all genotypes, seed and oil yields increased with increased growing season precipitation. Modern commercial cultivars of B. napus and B. juncea had the highest seed oil contents and generally produced the greatest oil yields across most environments, although they were not always the highest seed yielders. For instance, B. carinata over six site years in North Dakota and Minnesota yielded greater than B. napus producing as much as 2471 kg ha−1 in Minnesota. Camelina produced competitive seed yields in some of the drier environments and its δ13C signature indicated that it had the greatest drought resistance. However, seed oil content of some of these high yielding genotypes may need improvement before they are viable as biofuel feedstock.

Exploring Blueberry Aroma Complexity by Chromatographic and Direct-Injection Spectrometric Techniques.

Blueberry (Vaccinium spp.) fruit consumption has increased over the last 5 years, becoming the second most important soft fruit species after strawberry. Despite the possible economic and sensory impact, the blueberry volatile organic compound (VOC) composition has been poorly investigated. Thus, the great impact of the aroma on fruit marketability stimulates the need to step forward in the understanding of this quality trait. Beside the strong effect of ripening, blueberry aroma profile also varies due to the broad genetic differences among Vaccinium species that have been differently introgressed in modern commercial cultivars through breeding activity. In the present study, divided into two different activities, the complexity of blueberry aroma was explored by an exhaustive untargeted VOC analysis, performed by two complementary methods: SPME-GC-MS (solid phase microextraction- gas chromatography-mass spectrometry) and PTR-ToF-MS (proton transfer reaction-time of flight-mass spectrometry). The first experiment was aimed at determining the VOC modifications during blueberry ripening for five commercially representative cultivars (“Biloxi,” “Brigitta Blue,” “Centurion,” “Chandler,” and “Ozark Blue”) harvested at four ripening stages (green, pink, ripe, and over-ripe) to outline VOCs dynamic during fruit development. The objective of the second experiment was to confirm the analytical capability of PTR-ToF-MS to profile blueberry genotypes and to identify the most characterizing VOCs. In this case, 11 accessions belonging to different Vaccinium species were employed: V. corymbosum L. (“Brigitta,” “Chandler,” “Liberty,” and “Ozark Blue”), V. virgatum Aiton (“Centurion,” “Powder Blue,” and “Sky Blue”), V. myrtillus L. (three wild genotypes of different mountain locations), and one accession of V. cylindraceum Smith. This comprehensive characterization of blueberry aroma allowed the identification of a wide pull of VOCs, for the most aldehydes, alcohols, terpenoids, and esters that can be used as putative biomarkers to rapidly evaluate the blueberry aroma variations related to ripening and/or senescence as well as to genetic background differences. Moreover, the obtained results demonstrated the complementarity between chromatographic and direct-injection mass spectrometric techniques to study the blueberry aroma.

The two chromosomes of the mitochondrial genome of a sugarcane cultivar: assembly and recombination analysis using long PacBio reads.

Sugarcane accounts for a large portion of the worlds sugar production. Modern commercial cultivars are complex hybrids of S. officinarum and several other Saccharum species. Historical records identify New Guinea as the origin of S. officinarum and that a small number of plants originating from there were used to generate all modern commercial cultivars. The mitochondrial genome can be a useful way to identify the maternal origin of commercial cultivars. We have used the PacBio RSII to sequence and assemble the mitochondrial genome of a South East Asian commercial cultivar, known as Khon Kaen 3. The long read length of this sequencing technology allowed for the mitochondrial genome to be assembled into two distinct circular chromosomes with all repeat sequences spanned by individual reads. Comparison of five commercial hybrids, two S. officinarum and one S. spontaneum to our assembly reveals no structural rearrangements between our assembly, the commercial hybrids and an S. officinarum from New Guinea. The S. spontaneum, from India, and one sample of S. officinarum (unknown origin) are substantially rearranged and have a large number of homozygous variants. This supports the record that S. officinarum plants from New Guinea are the maternal source of all modern commercial hybrids.

Functional genomics of seed dormancy in wheat: advances and prospects.

Seed dormancy is a mechanism underlying the inability of viable seeds to germinate under optimal environmental conditions. To achieve rapid and uniform germination, wheat and other cereal crops have been selected against dormancy. As a result, most of the modern commercial cultivars have low level of seed dormancy and are susceptible to preharvest sprouting when wet and moist conditions occur prior to harvest. As it causes substantial loss in grain yield and quality, preharvest sprouting is an ever-present major constraint to the production of wheat. The significance of the problem emphasizes the need to incorporate an intermediate level of dormancy into elite wheat cultivars, and this requires detailed dissection of the mechanisms underlying the regulation of seed dormancy and preharvest sprouting. Seed dormancy research in wheat often involves after-ripening, a period of dry storage during which seeds lose dormancy, or comparative analysis of seeds derived from dormant and non-dormant cultivars. The increasing development in wheat genomic resources along with the application of transcriptomics, proteomics, and metabolomics approaches in studying wheat seed dormancy have extended our knowledge of the mechanisms acting at transcriptional and post-transcriptional levels. Recent progresses indicate that some of the molecular mechanisms are associated with hormonal pathways, epigenetic regulations, targeted oxidative modifications of seed mRNAs and proteins, redox regulation of seed protein thiols, and modulation of translational activities. Given that preharvest sprouting is closely associated with seed dormancy, these findings will significantly contribute to the designing of efficient strategies for breeding preharvest sprouting tolerant wheat.

Heterogeneity in the entire genome for three genotypes of peach [Prunus persica (L.) Batsch] as distinguished from sequence analysis of genomic variants

BackgroundPeach [Prunus persica (L.) Batsch] is an economically important fruit crop that has become a genetic-genomic model for all Prunus species in the family Rosaceae. A doubled haploid reference genome sequence length of 227.3 Mb, a narrow genetic base contrasted by a wide phenotypic variability, the generation of cultivars through hybridization with subsequent clonal propagation, and the current accessibility of many founder genotypes, as well as the pedigree of modern commercial cultivars make peach a model for the study of inter-cultivar genomic heterogeneity and its shaping by artificial selection.ResultsThe quantitative genomic differences among the three genotypes studied as genomic variants, included small variants (SNPs and InDels) and structural variants (SV) (duplications, inversions and translocations). The heirloom cultivar 'Georgia Belle’ and an almond by peach introgression breeding line 'F8,1-42’ are more heterogeneous than is the modern cultivar 'Dr. Davis’ when compared to the peach reference genome ('Lovell’). A pair-wise comparison of consensus genome sequences with 'Lovell’ showed that 'F8,1-42’ and 'Georgia Belle’ were more divergent than were 'Dr. Davis’ and 'Lovell’.ConclusionsA novel application of emerging bioinformatics tools to the analysis of ongoing genome sequencing project outputs has led to the identification of a range of genomic variants. Results can be used to delineate the genomic and phenotypic differences among peach genotypes. For crops such as fruit trees, the availability of old cultivars, breeding selections and their pedigrees, make them suitable models for the study of genome shaping by artificial selection. The findings from the study of such genomic variants can then elucidate the control of pomological traits and the characterization of metabolic pathways, thus facilitating the development of protocols for the improvement of Prunus crops.Electronic supplementary materialThe online version of this article (doi: 10.1186/1471-2164-14-750) contains supplementary material, which is available to authorized users.

Performance of Dry Bean Genotypes Grown under Organic and Conventional Production Systems in Michigan

The lack of data on the performance of dry bean (Phaseolus vulgaris L.) cultivars grown under organic management systems in Michigan prompted the evaluation of 32 diverse dry bean genotypes in side‐by‐side trials under organic and conventional production systems. Trial sites were located in grower fields in Gratiot County, in 2007 and 2008 and in Tuscola County in 2009 and at the Kellogg Biological Station in Kalamazoo County, in all 3 yr. The conventional plots were treated following standard acceptable management practices including application of granular fertilizer at planting and use of chemical seed treatments and foliar sprays to control pests. For the organic treatments certified organic land was used and only approved methods for organic production were followed. Rhizobium inoculant was applied to seeds in the organic treatment before planting. Yields were 20% higher in conventional systems than in the organic systems over all locations. Seed classes that yielded well in the organic system included pink‐, small red‐, and black‐seeded genotypes and these classes also had the highest accumulation of seed N (36%). Some genotypes appear better suited to organic production than others; however, those genotypes performing poorly under the organic system also performed poorly under conventional system. Overall genotypes of Andean origin performed 25% lower than genotypes of Middle American origin in either organic or conventional systems. Older cultivars, such as the heirloom navy bean Michelite, commonly believed to be better suited to organic production, did not perform as well as modern commercial cultivars.

Evolution of bread-making quality of Spanish bread-wheat genotypes

In this study, 36 Spanish wheat genotypes (five modern commercial cultivars, four cultivars introduced after the green revolution and 27 landraces from northwestern Spain) were evaluated. Grain (yield, specific weight, protein content and falling number) and flour (yield, protein content, Zeleny index, wet gluten and gluten index) properties were analyzed. Dough behaviour during mixing (DoughLAB) and handling (alveograph) was also considered. An evolution in grain and flour properties was observed over time. In modern cultivars, grain yield was improved owing to higher grain production. In landraces, higher grain yields were related to larger grain size. Unlike in landraces, an inverse correlation between grain yield and protein content was found in modern cultivars. In addition, because of their high protein quality, modern cultivars surpassed landraces in bread-making properties. Landraces showed considerable variability in protein quality and scored lower curve configuration ratio values than other cultivars with similar strength. Cultivars introduced after the green revolution reached the highest levels of bread-making quality, a feature attributable to their high protein quality.

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were pre-selected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P < 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (<0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of high-throughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.

Influence of Md-ACS1 allelotype and harvest season within an apple germplasm collection on fruit softening during cold air storage

Previous studies have demonstrated a relationship between Md-ACS1 allelotype and apple fruit softening at ambient temperatures. The present study was undertaken to further examine the influence of this allelotype ( -1/1, -1/2 or -2/2) and its interaction with harvest season (early or late) on changes in internal ethylene concentrations (IEC) and fruit softening during cold air storage. This was carried out by describing natural differences found among old apple cultivars/species and modern commercial cultivars. For late maturing cultivars, Md-ACS1-1/1 was firmer at harvest than Md-ACS1-2/2 with the heterozygote intermediate. However harvest firmness showed no differences among for the early season Md-ACS1 allelotypes. The Md-ACS1-2/2 allelotype had a slower rate of postharvest IEC increase and flesh softening compared with Md-ACS1-1/1 and -1/2 allelotypes, and late maturing cultivars had a slower rate of fruit softening than early maturing cultivars, which was independent of postharvest IEC. All three late season allelotypes and early season Md-ACS1-2/2 were firmer after storage than early season Md-ACS1-1/1 and -1/2 allelotypes, reflecting differences in both harvest firmness and softening rates . While cultivar variation in final firmness could be explained partially through Md-ACS1-mediated postharvest ethylene increases and subsequent softening, much more variation was accounted for by their differences in harvest firmness. These results are discussed in relation to strategies for breeding cultivars with superior flesh textures that are maintained during storage.