Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus

Most Rubus species have a biennial cycle of flowering and fruiting with an intervening period of winter dormancy, in common with many perennial fruit crops. Annual-fruiting (AF) varieties of raspberry (Rubus idaeus and Rubus occidentalis L.) and blackberry (Rubus subgenus Rubus) are able to flower and fruit in one growing season, without the intervening dormant period normally required in biennial-fruiting (BF) varieties. We used a red raspberry (R. idaeus) population segregating for AF obtained from a cross between NC493 and ‘Chilliwack’ to identify genetic factors controlling AF. Genotyping by sequencing (GBS) was used to generate saturated linkage maps in both parents. Trait mapping in this population indicated that AF is controlled by two newly identified loci (RiAF3 and RiAF4) located on Rubus linkage groups (LGs) 3 and 4. The location of these loci was analyzed using single-nucleotide polymorphism (SNP) markers on independent red raspberry and blackberry populations segregating for the AF trait. This confirmed that AF in Rubus is regulated by loci on LG 3 and 4, in addition to a previously reported locus on LG 7. Comparative RNAseq analysis at the time of floral bud differentiation in an AF and a BF variety revealed candidate genes potentially regulating the trait.info:eu-repo/semantics/publishedVersio

Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)

Understanding chromosome recombination behavior in polyploidy species is key to advancing genetic discoveries. In blueberry, a tetraploid species, the line of evidences about its genetic behavior still remain poorly understood, owing to the inter-specific, and inter-ploidy admixture of its genome and lack of in depth genome-wide inheritance and comparative structural studies. Here we describe a new high-quality, phased, chromosome-scale genome of a diploid blueberry, clone W85. The genome was integrated with cytogenetics and high-density, genetic maps representing six tetraploid blueberry cultivars, harboring different levels of wild genome admixture, to uncover recombination behavior and structural genome divergence across tetraploid and wild diploid species. Analysis of chromosome inheritance and pairing demonstrated that tetraploid blueberry behaves as an autotetraploid with tetrasomic inheritance. Comparative analysis demonstrated the presence of a reciprocal, heterozygous, translocation spanning one homolog of chr-6 and one of chr-10 in the cultivar Draper. The translocation affects pairing and recombination of chromosomes 6 and 10. Besides the translocation detected in Draper, no other structural genomic divergences were detected across tetraploid cultivars and highly inter-crossable wild diploid species. These findings and resources will facilitate new genetic and comparative genomic studies in Vaccinium and the development of genomic assisted selection strategy for this cro

Substantial and sustained reduction in under-5 mortality, diarrhea, and pneumonia in Oshikhandass, Pakistan : Evidence from two longitudinal cohort studies 15 years apart

Funding Information: Study 1 was funded through the Applied Diarrheal Disease Research Program at Harvard Institute for International Development with a grant from USAID (Project 936–5952, Cooperative Agreement # DPE-5952-A-00-5073-00), and the Aga Khan Health Service, Northern Areas and Chitral, Pakistan. Study 2 was funded by the Pakistan US S&T Cooperative Agreement between the Pakistan Higher Education Commission (HEC) (No.4–421/PAK-US/HEC/2010/955, grant to the Karakoram International University) and US National Academies of Science (Grant Number PGA-P211012 from NAS to the Fogarty International Center). The funding bodies had no role in the design of the study, data collection, analysis, interpretation, or writing of the manuscript. Publisher Copyright: © 2020 The Author(s).Peer reviewedPublisher PD

Identification of genetic regulators of longevity in dark-held detached Arabidopsis inflorescences : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology, Massey University, Palmerston North, New Zealand.

Harvested green plant tissues experience a number of stresses including energy deprivation, water disruption, and changes in hormone levels. These stresses accelerate the senescence of the tissues, which causes their deterioration. A comprehensive understanding of how these stresses cause senescence is essential if this unwanted deterioration is to be minimised. In this thesis, I used detached dark-held immature inflorescences of Arabidopsis thaliana (Arabidopsis) to investigate the regulatory programme responsible for the senescence of harvested energy-deprived tissue. Detached dark-held Arabidopsis inflorescences completely degreened at day 5 when held in the dark at 21°C. The degreening was accelerated by exogenously applying ACC, ethrel, MeJA, and ABA that have previously been shown to accelerate senescence in detached dark-held leaves. Higher MeJA concentrations unexpectedly delayed rather than accelerated degreening of the detached dark-held inflorescences and this was associated with reductions in transcripts for the senescence-associated genes SEN4, ANAC029, NAC3, and SAG12. To identify key genetic regulators of inflorescence senescence an untargeted forward genetics approach was utilized. This involved detaching the immature inflorescences grown from ~20,000 ethyl methane-sulfonate-treated (EMS-treated) Arabidopsis (Landsberg erecta) seeds, holding them in the dark at 21°C and visually identifying those that showed a different timing of degreening to wild type. This approach successfully identified inflorescences that were completely degreened at day 3 of dark incubation (two days earlier than wild type) that were designated accelerated inflorescence senescence (ais) and inflorescences that were more green than wild type at day 5 that were designated delayed inflorescences senescence (dis). A total of 10 ais and 20 dis mutants were identified. Interestingly, most of the dis mutants were specific for inflorescence senescence as they did not show delayed senescence in detached dark-held leaves. By utilizing a traditional map-based cloning approach, five dis mutants were mapped to particular chromosomal regions. dis9 was mapped to the top arm of chromosome 3, dis15 was to the bottom of chromosome 2, and dis1, dis34, and dis58 were mapped to chromosome 4. Whole genome sequencing of dis15 and 58 identified the EMS-induced lesions as G to A transitions in the eukaryotic ASPARTYL PROTEASE (AT2G28030) and NON-CODING RNA (AT4G13495), respectively. Transformation of the AT4G13495 DNA fragment into dis58 reverted the dis58 phenotype to wild-type confirming that the non-coding RNA is involved in regulating inflorescence senescence. In addition to these fertile mutants, a sterile agamouslike mutant that had a sepal-petal-petal phenotype was identified. The mutant showed delayed degreening of detached dark-held inflorescences. This prompted me to investigate the mechanism behind the delayed senescence of the sterile homeotic ag-1 mutant. The sepals of the ag-1 inflorescences were found to have both delayed in planta and detached dark-induced senescence. They were also found to be devoid of JA and like wild-type senesced when treated with MeJA. The delayed in planta sepal senescence appeared to be due to the lack of produced JA as the dde2 mutant (defective in JA biosynthesis and devoid of JA) also showed delayed in planta sepal senescence. However, the dde2 mutant did not show delayed darkinduced senescence suggesting that the delayed dark-induced senescence of ag-1 may be through a mechanism that is unrelated to the JA hormone. Taken together, in addition to identifying common regulators of inflorescence and leaf senescence, this screen has also identified novel regulators specific to inflorescence senescence that traditional screens based on leaf senescence would have missed. This suggests that there are both similarities and differences in the genetic pathways regulating leaf and inflorescence senescence. The identification of a range of mutants, some of which appear to be novel, also indicates that the immature detached Arabidopsis inflorescences are a useful system for studying energydeprivation driven senescence. Understanding the role of the dis58 non coding RNA and the other regulators in the mutant collection offers a new and exciting opportunity for ascertaining the regulatory genetic network initiated in energy-deprived tissues that control the deterioration of harvested produce

Arabidopsis AGAMOUS Regulates Sepal Senescence by Driving Jasmonate Production

The signal that initiates the age-regulated senescence program in flowers is still unknown. Here we propose for the ephemeral Arabidopsis thaliana flower that it dies because of continued expression of the MADS-box transcription factor AGAMOUS (AG). AG is necessary for specifying the reproductive structures of the flower. Flowers of ag-1, which lack AG, exhibited delayed sepal senescence and abscission. The flowers also had reduced jasmonic acid (JA) content. Other anther-defective sterile mutants deficient in JA, defective in anther dehiscence 1 (dad1) and delayed dehiscence 2 (dde2), exhibited delayed sepal senescence and abscission as well. Manually pollinated dad1 flowers produced siliques but still had delayed senescence, demonstrating that absence of pollination does not cause delayed senescence. When ag-1, dad1 and dde2 flowers were sprayed with 100 μM methyl jasmonate, the sepal senescence and abscission phenotypes were rescued, suggesting that JA has a role in these processes. Our study uncovers a novel role for AG in determining the timing of death of the flower it helps develop and highlights a role for JA in sepal senescence

Two loci, RiAF3 and RiAF4, contribute to the annual-fruiting trait in Rubus

Most Rubus species have a biennial cycle of flowering and fruiting with an intervening period of winter dormancy, in common with many perennial fruit crops. Annual-fruiting (AF) varieties of raspberry (Rubus idaeus and Rubus occidentalis L.) and blackberry (Rubus subgenus Rubus) are able to flower and fruit in one growing season, without the intervening dormant period normally required in biennial-fruiting (BF) varieties. We used a red raspberry (R. idaeus) population segregating for AF obtained from a cross between NC493 and ‘Chilliwack’ to identify genetic factors controlling AF. Genotyping by sequencing (GBS) was used to generate saturated linkage maps in both parents. Trait mapping in this population indicated that AF is controlled by two newly identified loci (RiAF3 and RiAF4) located on Rubus linkage groups (LGs) 3 and 4. The location of these loci was analyzed using single-nucleotide polymorphism (SNP) markers on independent red raspberry and blackberry populations segregating for the AF trait. This confirmed that AF in Rubus is regulated by loci on LG 3 and 4, in addition to a previously reported locus on LG 7. Comparative RNAseq analysis at the time of floral bud differentiation in an AF and a BF variety revealed candidate genes potentially regulating the trait.This project was funded by New Zealand Ministry of Business Innovation and Employment (MBIE) Strategic Science Investment Fund (SSIF) allocated to Plant & Food Research as part of the Discovery Science programs.Peer reviewe

Two Loci, RiAF3 and RiAF4, Contribute to the Annual-Fruiting Trait in Rubus

Most Rubus species have a biennial cycle of flowering and fruiting with an intervening period of winter dormancy, in common with many perennial fruit crops. Annual-fruiting (AF) varieties of raspberry (Rubus idaeus and Rubus occidentalis L.) and blackberry (Rubus subgenus Rubus) are able to flower and fruit in one growing season, without the intervening dormant period normally required in biennial-fruiting (BF) varieties. We used a red raspberry (R. idaeus) population segregating for AF obtained from a cross between NC493 and 'Chilliwack' to identify genetic factors controlling AF. Genotyping by sequencing (GBS) was used to generate saturated linkage maps in both parents. Trait mapping in this population indicated that AF is controlled by two newly identified loci (RiAF3 and RiAF4) located on Rubus linkage groups (LGs) 3 and 4. The location of these loci was analyzed using single-nucleotide polymorphism (SNP) markers on independent red raspberry and blackberry populations segregating for the AF trait. This confirmed that AF in Rubus is regulated by loci on LG 3 and 4, in addition to a previously reported locus on LG 7. Comparative RNAseq analysis at the time of floral bud differentiation in an AF and a BF variety revealed candidate genes potentially regulating the trait

Carbon deprivation-driven transcriptome reprogramming in detached developmentally arresting Arabidopsis inflorescences

Senescence is genetically controlled and activated in mature tissues during aging. However, immature plant tissues also display senescence-like symptoms when continuously exposed to adverse energy-depleting conditions. We used detached dark-held immature inflorescences of Arabidopsis (Arabidopsis thaliana) to understand the metabolic reprogramming occurring in immature tissues transitioning from rapid growth to precocious senescence. Macroscopic growth of the detached inflorescences rapidly ceased upon placement in water in the dark at 21°C. Inflorescences were completely degreened by 120 h of dark incubation and by 24 h had already lost 24% of their chlorophyll and 34% of their protein content. Comparative transcriptome profiling at 24 h revealed that inflorescence response at 24 h had a large carbon-deprivation component. Genes that positively regulate developmental senescence (ARABIDOPSIS NAC DOMAIN CONTAINING PROTEIN92) and shade-avoidance syndrome (PHYTOCHROME INTERACTING FACTOR4 [PIF4] and PIF5) were up-regulated within 24 h. Mutations in these genes delayed degreening of the inflorescences. Their up-regulation was suppressed in dark-held inflorescences by glucose treatment, which promoted macroscopic growth and development and inhibited degreening of the inflorescences. Detached inflorescences held in the dark for 4 d were still able to reinitiate development to produce siliques upon being brought out to the light, indicating that the transcriptional reprogramming at 24 h was adaptive and reversible. Our results suggest that the response of detached immature tissues to dark storage involves interactions between carbohydrate status sensing and light deprivation signaling and that the dark-adaptive response of the tissues appears to utilize some of the same key regulators as developmental senescence