Insights into the novel members of the FAD2 gene family involved in high-oleate fluxes in peanut.

The FAD2 gene family is functionally responsible for the conversion of oleic acid to linoleic acid in oilseed plants. Multiple members of the FAD gene are known to occur in several oilseed species. In this study, six novel full-length cDNA sequences (named as AhFAD2-1, -2, -3, -4, -5, and -6) were identified in peanut (Arachis hypogaea L.), an analysis of which revealed open reading frames of 379, 383, 394, or 442 amino acids. Sequence comparisons showed that AhFAD2-1 and AhFAD2-2 shared 76% identity, while AhFAD2-2, -3, and -4 displayed highly significant homology. There was only 27% identity overlap between the microsomal ω-6 fatty acid desaturase and the chloroplast ω-6 fatty acid desaturase encoded by AhFAD2-1, -2, -3, -4, and AhFAD2-5, -6, respectively. The phylogeny tree of FAD2 transcripts showed five major groups, and AhFAD2-1 was clearly separated from other groups. Analysis of AhFAD2-1 and AhFAD2-2 transcript distribution in different peanut tissues showed that the AhFAD2-1 gene showed upward of a 70-fold increase in expression of fatty acid than the AhFAD2-2 gene in peanut developing seeds, while the AhFAD2-2 gene expressed most abundantly in peanut flowers. Because the AhFAD2-1 gene played a major role in the conversion of oleic to linoleic acid during seed development, the identification of this novel member in this study would facilitate the further genetic manipulation of peanut oil quality. The implications of overall results also suggest that there may be more candidate genes controlling levels of oleate acid in developing seeds. Results also may be due to the presence of complex gene networks controlling the fluxes between the endoplasmic reticulum and the chloroplast within the peanut cells.

Phylogenetic relationships of species of genus Arachis based on genic sequences.

The genus Arachis (Fabaceae), which originated in South America, consists of 80 species. Based on morphological traits and cross-compatibility among the species, the genus is divided into nine taxonomic sections. Arachis is the largest section including the economically valuable cultivated peanut (A. hypogaea). Seven genic sequences were utilized to better understand the phylogenetic relationships between species of genus Arachis. Our study displayed four clades of species of Arachis. Arachis triseminata was genetically isolated from all other species of Arachis studied, and it formed the basal clade with A. retusa and A. dardani from the most ancient sections Extranervosae and Heteranthae, respectively. Species of section Arachis formed a separated single clade from all other species, within which species having B and D genome clustered in one subgroup and three species characterized with an A genome grouped together in another subgroup. A divergent clade including species from five sections was sister to the clade of section Arachis. Between the sister clades and the basal clade there was a clade containing species from the more advanced sections. Phylogenetic relationships of all the species of Arachis using multiple genic sequences were similar to the phylogenies produced with single-copy genes.

Identification and characterization of gene-based SSR markers in date palm (Phoenix dactylifera L.).

BACKGROUND: Date palm (Phoenix dactylifera L.) is an important tree in the Middle East and North Africa due to the nutritional value of its fruit. Molecular Breeding would accelerate genetic improvement of fruit tree through marker assisted selection. However, the lack of molecular markers in date palm restricts the application of molecular breeding. RESULTS: In this study, we analyzed 28,889 EST sequences from the date palm genome database to identify simple-sequence repeats (SSRs) and to develop gene-based markers, i.e. expressed sequence tag-SSRs (EST-SSRs). We identified 4,609 ESTs as containing SSRs, among which, trinucleotide motifs (69.7%) were the most common, followed by tetranucleotide (10.4%) and dinucleotide motifs (9.6%). The motif AG (85.7%) was most abundant in dinucleotides, while motifs AGG (26.8%), AAG (19.3%), and AGC (16.1%) were most common among trinucleotides. A total of 4,967 primer pairs were designed for EST-SSR markers from the computational data. In a follow up laboratory study, we tested a sample of 20 random selected primer pairs for amplification and polymorphism detection using genomic DNA from date palm cultivars. Nearly one-third of these primer pairs detected DNA polymorphism to differentiate the twelve date palm cultivars used. Functional categorization of EST sequences containing SSRs revealed that 3,108 (67.4%) of such ESTs had homology with known proteins. CONCLUSION: Date palm EST sequences exhibits a good resource for developing gene-based markers. These genic markers identified in our study may provide a valuable genetic and genomic tool for further genetic research and varietal development in date palm, such as diversity study, QTL mapping, and molecular breeding.

Assessment of Caregiving Burden of Family Caregivers of Advanced Cancer Patients and Their Satisfaction with the Dedicated Inpatient Palliative Care Provided to Their Patients: A Cross-Sectional Study from a Tertiary Care Centre in South Asia.

BACKGROUND AND OBJECTIVES: Family Caregivers (FCs) of advanced cancer patients often suffer from caregiving burden due to stress arising from the responsibility of caregiving. During the course of their patients palliative therapy, FCs quality of life seems to be influenced by their satisfaction with the quality of patient care. In this study, caregiving burden of FCs and their satisfaction with dedicate Inpatient palliative care (IPC) services provided to their patients  were studied. MATERIAL AND METHODS: This cross-sectional study assessed 211 FCs of advanced cancer patients. Caregiving burden of FCs and their satisfaction with IPC were studied through Zarith Burden Interview (ZBI-12 version) and Family Carer Satisfaction with Palliative Care scale (FAMCARE-2)  questionnaires, respectively. Descriptive and correlation analyses were deployed for data analysis. RESULTS: The summative mean ZBI-12 score for FCs was 20.26±5.92, suggesting moderate to high caregiving burden among FCs. Significantly higher scores were observed among FCs who belonged to below poverty line (BPL) families(p=0.025), revealing higher caregiving burden among this lower income group. FCs who were male, unmarried, unemployed, and residing in rural experienced higher caregiving burden. However, it did not lead to a statistically significant difference. The summative mean FAMCARE-2 scale scores was 74.01±4.34, which suggested FCs high satisfaction with the palliative care services provided to their patients. FAMCARE-2 scale scores were lower for BPL families, but it was not statistically significant. CONCLUSION: FCs from lower-income groups experienced higher caregiving burden. It seems that IPC unit provided satisfactory services to advanced cancer patients, leading to enhancement of FCs satisfaction and consequently quality of life. 
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Evaluation of peanut genotypes for in vitro plant regeneration using thidiazuron.

A major limitation with the available protocols for in vitro regeneration of peanut (Arachis hypogaea L.) is their narrow application to very few select genotypes. Here, we report a protocol that can be applied across a broad spectrum of peanut market types, explant types and geographic regions using thidiazuron (TDZ). The effect of the timing of TDZ application to the culturing of both zygotic embryos and subsequent plantlet explants on MS medium is also reported. An extended use of TDZ and at a higher concentration (30 m/l) resulted in the greatest explant shoot average (approximately 13). However, a limited application of TDZ (10 d) was sufficient to induce shoot formation in peanut. Hypocotyl was the best explant type that induced the greatest shoot average (15) across market types followed by lamina (7.4). Spanish and Valencia were the most efficient market groups that induced shoots across explant types, consistently.

QTL mapping for bacterial wilt resistance in peanut (Arachis hypogaea L.).

Bacterial wilt (BW) caused by Ralstonia solanacearum is a serious, global, disease of peanut (Arachis hypogaea L.), but it is especially destructive in China. Identification of DNA markers linked to the resistance to this disease will help peanut breeders efficiently develop resistant cultivars through molecular breeding. A F2 population, from a cross between disease-resistant and disease-susceptible cultivars, was used to detect quantitative trait loci (QTL) associated with the resistance to this disease in the cultivated peanut. Genome-wide SNPs were identified from restriction-site-associated DNA sequencing tags using next-generation DNA sequencing technology. SNPs linked to disease resistance were determined in two bulks of 30 resistant and 30 susceptible plants along with two parental plants using bulk segregant analysis. Polymorphic SSR and SNP markers were utilized for construction of a linkage map and for performing the QTL analysis, and a moderately dense linkage map was constructed in the F2 population. Two QTL (qBW-1 and qBW-2) detected for resistance to BW disease were located in the linkage groups LG1 and LG10 and account for 21 and 12 % of the bacterial wilt phenotypic variance. To confirm these QTL, the F8 RIL population with 223 plants was utilized for genotyping and phenotyping plants by year and location as compared to the F2 population. The QTL qBW-1 was consistent in the location of LG1 in the F8 population though the QTL qBW-2 could not be clarified due to fewer markers used and mapped in LG10. The QTL qBW-1, including four linked SNP markers and one SSR marker within 14.4-cM interval in the F8, was closely related to a disease resistance gene homolog and was considered as a candidate gene for resistance to BW. QTL identified in this study would be useful to conduct marker-assisted selection and may permit cloning of resistance genes. Our study shows that bulk segregant analysis of genome-wide SNPs is a useful approach to expedite the identification of genetic markers linked to disease resistance traits in the allotetraploidy species peanut.

Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.).

BACKGROUND: Genomic research of cultivated peanut has lagged behind other crop species because of the paucity of polymorphic DNA markers found in this crop. It is necessary to identify additional DNA markers for further genetic research in peanut. RESULTS: Microsatellite markers in cultivated peanut were developed using the SSR enrichment procedure. The results showed that the GA/CT repeat was the most frequently dispersed microsatellite in peanut. The primer pairs were designed for fifty-six different microsatellites, 19 of which showed a polymorphism among the genotypes studied. The average number of alleles per locus was 4.25, and up to 14 alleles were found at one locus. This suggests that microsatellite DNA markers produce a higher level of DNA polymorphism than other DNA markers in cultivated peanut. CONCLUSIONS: It is desirable to isolate and characterize more DNA markers in cultivated peanut for more productive genomic studies, such as genetic mapping, marker-assisted selection, and gene discovery. The development of microsatellite markers holds a promise for such studies.

An evaluation of new gel matrices for the separation of PCR-amplified DNA fragments.

It has been shown that the novel gel matrix, PCR Purity Plus which consists of a vinyl-polymer of polyacrylamide, provides a superior and rapid means of separating DNA fragments. As this product has been discontinued, the two new commercial versions of this matrix (MDE and GeneAmp) with PCR Purity Plus were compared. Optimal conditions for resolving DNA fingerprint profiles for both matrices were defined. Both MDE and GeneAmp gels provided a clear separation of DNA fragments. However, the profiles obtained on GeneAmp gel were closest to that of PCR Purity Plus. These results should be useful to DNA fingerprinting studies where it is critical to obtain a clear resolution of complex DNA profiles.

Genetic transformation of sweet potato by particle bombardment.

Transient and stable expression of foreign genes has been achieved in sweet potato using the particle bombardment system of gene delivery. Callus and root isolates of two genotypes (Jewel and TIS-70357) with positive signs of transformation have been recovered. Tungsten microcarriers coated with plasmid DNA (pBI 221 containing the gusA gene) were accelerated at high velocity using a biolistic device into sweet potato target tissues. Histochemical examination of bombarded leaf and petiole explants revealed that most had cells expressing the gusA gene. When explants were cultured, calli and roots developed in most bombarded tissues. Similar results but with a lower frequency of transformation were observed when the plasmid pBI 121 (with gusA and antibiotic resistance npt II genes) was employed and bombarded explants cultured on an antibiotic selection medium. Subcultured roots and calli were positive for gusA expression when tested even after one year of in vitro culture, and thus the expression of the foreign gene is fairly stable. The particle bombardment approach of gene delivery appears to have a potential for generating transgenic sweet potatoes with useful agronomic traits.

Analysis of genetic diversity in a sweetpotato (Ipomoea batatas) germplasm collection using DNA amplification fingerprinting.

A DNA amplification fingerprinting (DAF) approach was employed to develop individual-specific profiles and analyze genetic relationships among 73 plant introductions of sweetpotato (Ipomoea batatas (L.) Lam.) including unadapted lines from around the world and a few selected U.S.A. cultivars. Reliable and informative fingerprint profiles were obtained employing single octamer primers and Stoffel fragment Taq polymerase in the polymerase chain reaction, polyacrylamide-based vinyl polymer for electrophoresis, and silver staining to visualize the DNA. Using seven highly informative octamer primers, individual-specific DAF profiles were obtained for all accessions tested. The degree of polymorphism in the sweetpotato collection was very large, indicating a high level of genetic variability. Several accessions clustered together based on their geographic source. Most U.S.A. cultivars formed a separate cluster in the phenogram, while accessions from Papua New Guinea exhibited the highest genetic diversity. The wild species I. triloba and tetraploid I. batatas formed a group distinct from the cultivated sweetpotato. DAF appears to be useful in sweetpotato germplasm characterization and may be employed to identify duplicate accessions or for creation of core subsets. DAF data may also be useful for facilitating the selection of parents for a breeding program to ensure a broad genetic base.

Thidiazuron promotes high frequency regeneration of peanut (Arachis hypogaea) plants in vitro.

Multiple shoots were induced on Valenciatype peanut (Arachis hypogaea L.) explants cultured in vitro on a nutrient medium supplemented with thidiazuron. Zygotic embryos excised from mature seeds were germinated on Murashige-Skoog nutrient medium, and the resulting plantlets (8 days-old) were used as a source of explants. When cultured on a nutrient medium with increasing levels of thidiazuron (0.5 to 30 mg/l), expiants from various parts of the peanut plant (except the root) produced multiple shoot primordia which subsequently developed into individual shoots. Hypocotyl and cotyledon explants produced shoots in higher numbers than other explants (20 shoots per hypocotyl explant at all thidiazuron concentrations and 15 shoots per cotyledon explant at 30 mg/l). Shoots rooted normally on a basal Murashige-Skoog medium containing charcoal and developed into healthy and fertile plants when planted in soil.

Rapid and repetitive plant regeneration in sweetpotato via somatic embryogenesis.

An efficient in vitro plant regeneration system characterized by rapid and continuous production of somatic embryos using leaf and petiole expiants has been developed in sweetpotato [Ipomoea batatas L. (Lam.)]. The optimal somatic embryogenic response was obtained in the genotype PI 318846-3 with a two-step protocol: (1) stage I-incubation of expiants in the dark for 2 weeks on Murashige Skoog (MS) medium containing 2,4-dichlorophenoxyacetic acid (2,4-D) (2.5 mg/l) and 6-benzylaminopurine (0.25 mg/l) and, (2) stage II-culture in the light on MS medium with abscisic acid (ABA) (2.5 mg/l). The addition of ABA was critical for enhanced production of somatic embryos. Secondary somatic embryos were produced from the primary embryos cultured on MS medium with 2,4-D at 0.2 mg/l. The somatic embryos were converted into normal plantlets when cultured on basal MS medium. Upon transfer to soil, plants grew well and appeared normal with no mortality. The system of somatic embryogenesis described here will facilitate tissue culture, germplasm conservation and gene transfer research of sweetpotato due to its rapidity (6 to 10 weeks), prolific plant production by direct embryogenesis, ease of secondary somatic embryo production and reproducibility.

Analysis of genetic diversity in Chinese sweetpotato [Ipomoea batatas (L.) Lam.] germplasm using DNA amplification fingerprinting.

The genetic diversity and evolutionary relationships in a representative sample of Chinese sweetpotato collection were assessed using the DNA amplification fingerprinting approach. DNA fingerprint profiles were developed for all 42 accessions tested. There were 19-26 bands for each accession and an average of 20.7 such bands were polymorphic. Chinese sweetpotato germplasm tested exhibited a high degree of genetic diversity. Phenetic analysis revealed five major clusters with the following components: (1) landraces from Guangdong Province, (2) landraces from Fujian province, (3) Chinese cultivars, (4) those closely related to Japanese sweetpotato cultivars, and (5) those closely related to the US sweetpotato cv. Nancy Hall. The genetic association observed between accessions was largely consistent with the known pedigree records. The DNA amplification fingerprinting may provide reliable insights into the domestication history of the sweetpotato crop and may be useful in germplasm enhancement.