Genome-Wide Association Study and Genomic Prediction of Fusarium Wilt Resistance in Common Bean Core Collection.

The common bean (Phaseolus vulgaris L.) is a globally cultivated leguminous crop. Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. phaseoli (Fop), is a significant disease leading to substantial yield loss in common beans. Disease-resistant cultivars are recommended to counteract this. The objective of this investigation was to identify single nucleotide polymorphism (SNP) markers associated with FW resistance and to pinpoint potential resistant common bean accessions within a core collection, utilizing a panel of 157 accessions through the Genome-wide association study (GWAS) approach with TASSEL 5 and GAPIT 3. Phenotypes for Fop race 1 and race 4 were matched with genotypic data from 4740 SNPs of BARCBean6K_3 Infinium Bea Chips. After ranking the 157-accession panel and revealing 21 Fusarium wilt-resistant accessions, the GWAS pinpointed 16 SNPs on chromosomes Pv04, Pv05, Pv07, Pv8, and Pv09 linked to Fop race 1 resistance, 23 SNPs on chromosomes Pv03, Pv04, Pv05, Pv07, Pv09, Pv10, and Pv11 associated with Fop race 4 resistance, and 7 SNPs on chromosomes Pv04 and Pv09 correlated with both Fop race 1 and race 4 resistances. Furthermore, within a 30 kb flanking region of these associated SNPs, a total of 17 candidate genes were identified. Some of these genes were annotated as classical disease resistance protein/enzymes, including NB-ARC domain proteins, Leucine-rich repeat protein kinase family proteins, zinc finger family proteins, P-loopcontaining nucleoside triphosphate hydrolase superfamily, etc. Genomic prediction (GP) accuracy for Fop race resistances ranged from 0.26 to 0.55. This study advanced common bean genetic enhancement through marker-assisted selection (MAS) and genomic selection (GS) strategies, paving the way for improved Fop resistance.

Plio-Pleistocene deep-sea ventilation in the eastern Pacific and potential linkages with Northern Hemisphere glaciation.

Antarctic bottom water (AABW) production is a key factor governing global ocean circulation, and the present disintegration of the Antarctic Ice Sheet slows it. However, its long-term variability has not been well documented. On the basis of high-resolution chemical scanning of a well-dated marine ferromanganese nodule from the eastern Pacific, we derive a record of abyssal ventilation spanning the past 4.7 million years and evaluate its linkage to AABW formation over this period. We find that abyssal ventilation was relatively weak in the early Pliocene and persistently intensified from 3.4 million years ago onward. Seven episodes of markedly reduced ocean ventilation indicative of AABW formation collapse are identified since the late Pliocene, which were accompanied by key stages of Northern Hemisphere glaciation. We suggest that the interpolar climate synchronization within these inferred seven collapse events may have intensified global glaciation by inducing poleward moisture transport in the Northern Hemisphere.

Upper Norian conodonts from the Baoshan block, western Yunnan, southwestern China, and implications for conodont turnover.

The Sevatian of the late Norian is one of the key intervals in biotic turnover and in changes of paleoclimate and paleoenvironments. Conodont faunas recovered from two sections of upper Norian strata of the Dashuitang and Nanshuba formations near Baoshan City in western Yunnan province provide new insights into the diversity and biostratigraphy of the Sevatian conodonts within China as well as globally. A lower Mockina (M.) bidentata Zone and an upper Parvigondolella (P.) andrusovi Zone are identified in this area according to the first occurrences of M. bidentata and of P. andrusovi. Rich conodont fauna of M. zapfei is detailed and presents various intraspecific forms. A total of 19 forms of P1 elements are presented, which, when combined with the reported conodonts in the M. bidentata Zone, suggest that there was a peak in conodont diversity within the M. bidentata Zone. A biotic crisis in the uppermost M. bidentata Zone is recognized from the contrast between the diverse conodont fauna in the M. bidentata Zone and the rare conodonts in the P. andrusovi Zone. The conodont turnover during the middle Sevatian highlights the fact that the prolonged phases of the end-Triassic mass extinction probably began in the transition interval from M. bidentata Zone to P. andrusovi Zone.

Cyclostratigraphy and astrochronology: Case studies from China.

A high-precision geologic time scale is the essential key for understanding the Earth's evolutionary history and geologic processes. Astronomical tuning of orbitally forced stratigraphic records to construct high-resolution Astronomical Time Scales (ATS) has led to a progressive refinement of the geologic time scale over the past two decades. In turn, these studies provide new insights regarding the durations and rates of major Earth events, evolutionary processes, and climate changes, all of which provide a scientific basis for contextualizing and predicting future global change trends. South China hosts some of the best-exposed and well-dated Neoproterozoic through Mesozoic stratigraphic sections in the world; many of which are suitable for cyclostratigraphy and calibrating the geologic time scale. In North China, several Cenozoic oil-bearing basins have deep boreholes with continuous sampling and/or well logging that enable derivation of astronomically tuned time scales for an improved understanding of basin evolution and hydrocarbon generation. This Special Issue focuses on case studies of astrochronology and applied cyclostratigraphy research using reference sections within China. In this introductory overview, we: (1) summarize all existing astrochronology studies of the Neoproterozoic through Cenozoic sections within China that have been used to enhance the international geologic time scale, (2) examine briefly the astronomically forced paleoclimate information recorded in various depositional systems and the modern techniques employed to analyze the periodicity of these signals encoded within the sedimentary record, and (3) summarize the 20 contributions to this Special Issue of Palaeogeography, Palaeoclimatology, Palaeoecology on 'Cyclostratigraphy and Astrochronology: Case studies from China'.

Integrated species-phenon trees: visualizing infraspecific diversity within lineages.

The unprecedented detail with which contemporary molecular phylogenetics are visualizing infraspecific relationships within living species and species complexes cannot as yet be reliably extended into deep time. Yet paleontological systematics has routinely dealt in (mainly) morphotaxa envisaged in various ways to have been components of past species lineages. Bridging these perspectives can only enrich both. We present a visualization tool that digitally depicts infraspecific diversity within species through deep time. Our integrated species-phenon tree merges ancestor-descendant trees for fossil morphotaxa (phena) into reconstructed phylogenies of lineages (species) by expanding the latter into "species boxes" and placing the phenon trees inside. A key programming strategy to overcome the lack of a simple overall parent-child hierarchy in the integrated tree has been the progressive population of a species-phenon relationship map which then provides the graphical footprint for the overarching species boxes. Our initial case has been limited to planktonic foraminfera via Aze & others' important macroevolutionary dataset. The tool could potentially be appropriated for other organisms, to detail other kinds of infraspecific granularity within lineages, or more generally to visualize two nested but loosely coupled trees.

Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011).

The unique macroevolutionary dataset of Aze & others has been transferred onto the TimeScale Creator visualisation platform while, as much as practicable, preserving the original unrevised content of its morphospecies and lineage evolutionary trees. This is a "Corrected Version" (not a revision), which can serve as an on-going historical case example because it is now updatable with future time scales. Both macroevolutionary and biostratigraphic communities are now equipped with an enduring phylogenetic database of Cenozoic macroperforate planktonic foraminiferal morphospecies and lineages for which both graphics and content can be visualised together. Key to maintaining the currency of the trees has been specification of time scales for sources of stratigraphic ranges; these scales then locate the range dates within the calibration series. Some ranges or their sources have undergone mostly minor corrections or amendments. Links between lineage and morphospecies trees have been introduced to improve consistency and transparency in timing within the trees. Also, Aze & others' dual employment of morphospecies and lineage concepts is further elaborated here, given misunderstandings that have ensued. Features displayed on the trees include options for line styles for additional categories for range extensions or degrees of support for ancestor-descendant proposals; these have been applied to a small number of instances as an encouragement to capture more nuanced data in the future. In addition to labeling of eco- and morpho-groups on both trees, genus labels can be attached to the morphospecies tree to warn of polyphyletic morphogenera, and the lineage codes have been decoded to ease their recognition. However, it is the mouse-over pop-ups that provide the greatest opportunity to embed supporting information in the trees. They include details for stratigraphic ranges and their recalibration steps, positions relative to the standard planktonic-foraminiferal zonation, and applications as datums, as well as mutual listings between morphospecies and lineages which ease the tracing of their interrelated contents. The elaboration of the original dataset has been captured in a relational database, which can be considered a resource in itself, and, through queries and programming, serves to generate the TimeScale Creator datapacks.

Sedimentary noise and sea levels linked to land-ocean water exchange and obliquity forcing.

In ancient hothouses lacking ice sheets, the origins of large, million-year (myr)-scale sea-level oscillations remain a mystery, challenging current models of sea-level change. To address this mystery, we develop a sedimentary noise model for sea-level changes that simultaneously estimates geologic time and sea level from astronomically forced marginal marine stratigraphy. The noise model involves two complementary approaches: dynamic noise after orbital tuning (DYNOT) and lag-1 autocorrelation coefficient (ρ1). Noise modeling of Lower Triassic marine slope stratigraphy in South China reveal evidence for global sea-level variations in the Early Triassic hothouse that are anti-phased with continental water storage variations in the Germanic Basin. This supports the hypothesis that long-period (1-2 myr) astronomically forced water mass exchange between land and ocean reservoirs is a missing link for reconciling geological records and models for sea-level change during non-glacial periods.

Astronomical time scale for the lower Doushantuo Formation of early Ediacaran, South China.

Nearly 90% of the Ediacaran Period (635-541 Ma) of the Neoproterozoic is represented by the Doushantuo Formation (DST Fm) in South China. Its lowest Member I is a 3.7 m-thick cap carbonate deposited at the termination of the Cryogenian Marinoan glaciation. The DST Fm consists of alternating organic-rich black shale and thinly bedded dolostone, and it contains some of the oldest records of multi-cellular life and three pronounced negative carbon isotope excursions. The Jiulongwan (JLW) section is a well-studied reference section for these Ediacaran events. Spectral analysis of geochemical data through the lower DST Fm (22.3 m) shows 27 predominant ∼90 cm sedimentary cycles that correspond to 405-ka long eccentricity cycles. The power spectra of the 405-ka tuned Ca and Fe/Ti series show significant peaks at ∼1.2-Ma, 405-ka, 133-ka, 128-ka, 100-ka, 82-ka, ∼31-ka and 29-ka periods, respectively. A 11.16 Ma-long astronomical time scale has been constructed for the lower DST Fm and provide a duration of 1.6 Ma for the cap carbonate (Member I) based on the 405-ka long eccentricity cycle tuning. Using the U-Pb age of 635.2 ±â€¯0.6 Ma for the volcanic ash bed at the Member I/II boundary, we proposed a 636.8 Ma age for the base of the DST Fm. These ages and astronomical timescale provide important new constraints on the subdivision of Ediacaran strata, and have implications for understanding the character of the first negative δ13C excursion (EN1). Orbital forcing may have been played an important role for the climate changes and the evolution of Ediacaran multi-cellular life and the carbon cycle variations.