Advances in next generation sequencing technologies and statistical approaches enable genome-wide dissection of phenotypic traits via genome-wide association studies (GWAS). Although multiple ...statistical approaches for conducting GWAS are available, the power and cross-validation rates of many approaches have been mostly tested using simulated data. Empirical comparisons of single variant (SV) and multi-variant (MV) GWAS approaches have not been conducted to test if a single approach or a combination of SV and MV is effective, through identification and cross-validation of trait-associated loci. In this study, kernel row number (KRN) data were collected from a set of 6,230 entries derived from the Nested Association Mapping (NAM) population and related populations. Three different types of GWAS analyses were performed: 1) single-variant (SV), 2) stepwise regression (STR) and 3) a Bayesian-based multi-variant (BMV) model. Using SV, STR, and BMV models, 257, 300, and 442 KRN-associated variants (KAVs) were identified in the initial GWAS analyses. Of these, 231 KAVs were subjected to genetic validation using three unrelated populations that were not included in the initial GWAS. Genetic validation results suggest that the three GWAS approaches are complementary. Interestingly, KAVs in low recombination regions were more likely to exhibit associations in independent populations than KAVs in recombinationally active regions, probably as a consequence of linkage disequilibrium. The KAVs identified in this study have the potential to enhance our understanding of the genetic basis of ear development.
The town of Kobarid is located in one of three areas with the highest seismic hazard in Slovenia. It was hit by several 1976–1977 Friuli sequence earthquakes and recently by the 1998 and 2004 Krn ...Mountains earthquakes which caused damage of intensity up to VII EMS-98 scale. The town is located in a small basin filled with heterogeneous glaciofluvial Quaternary sediments in which site effects due to soft sediments are expected. The existing microzonation which is based on surface geological data only is inadequate, and no borehole or geophysical data are available in the basin that would allow a modelling approach of site effects assessment. The microtremor horizontal-to-vertical spectral ratio (HVSR) method was therefore applied in order to assess the fundamental frequency of the sediments. Investigations were performed on a 100×100 m dense grid and 106 free-field measurements acquired. Clear HVSR peaks were obtained in the majority of the surveyed area. The eastern part of the basin is characterized by two well separated peaks which indicate distinct shallow and deep impedance contrasts. The iso-frequency map of sediments shows a distribution in a broad range of 1.8–22.2 Hz. The observed frequencies can be related to the total thickness of Quaternary sediments (sand, gravel) in the western part of the basin only. They are deposited over bedrock built of Cretaceous flysch. In the eastern part the obtained fundamental frequencies are influenced by the presence of a shallow conglomerate layer inside sandy gravel or lacustrine chalk. The extent of these layers was not known before. Microtremor measurements were also performed inside 19 characteristic buildings of various heights (from two to four stories), and longitudinal and transverse fundamental frequencies determined from amplitude spectra. A potential of soil-structure resonance was assessed by comparing building frequencies with the free-field sediments frequencies derived from the iso-frequency map. For two surveyed buildings a high danger of soil-structure resonance was assessed and for three buildings the danger was of medium level. The building resonant frequency of two- and three-story houses, which prevail in the area, spans the range 4–11 Hz, with an average value of 7.7 Hz. The danger of soil-structure resonance should be therefore sought in this frequency range. Since the majority of Kobarid area is characterized by lower (W part) or higher (E part) frequencies, the danger exist mainly in a relatively narrow transition zone.
Kernel row number (KRN) is a crucial trait in maize that directly influences yield; hence, understanding the mechanisms underlying KRN is vital for the development of high-yielding inbred lines and ...hybrids. We crossed four excellent panicle inbred lines (CML312, CML444, YML46, and YML32) with Ye107, and after eight generations of selfing, a multi-parent population was developed comprising four subpopulations, each consisting of 200 lines. KRN was accessed in five environments in Yunnan province over three years (2019, 2021, and 2022). The objectives of this study were to (1) identify quantitative trait loci and single nucleotide polymorphisms associated with KRN through linkage and genome-wide association analyses using high-quality genotypic data, (2) identify candidate genes regulating KRN by identifying co-localized QTLs and SNPs, and (3) explore the pathways involved in KRN formation and identify key candidate genes through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Our study successfully identified 277 significant Quantitative trait locus (QTLs) and 53 significant Single Nucleotide Polymorphism (SNPs) related to KRN. Based on gene expression, GO, and KEGG analyses, SNP-177304649, SNP-150393177, SNP-135283055, SNP-138554600, and SNP-120370778, which were highly likely to be associated with KRN, were identified. Seven novel candidate genes at this locus (
,
,
,
,
,
, and
) are associated with KRN. Among these,
was identified using the reference genome Mo17. The remaining six genes were identified using the reference genome B73. To our knowledge, this is the first report on the association of these genes with KRN in maize. These findings provide a theoretical foundation and valuable insights into the genetic mechanisms underlying maize KRN and the development of high-yielding hybrids through heterosis.
Maize kernel row number (KRN) is one of the most important yield traits and has changed greatly during maize domestication and selection. Elucidating the genetic basis of KRN will be helpful to ...improve grain yield in maize. Here, we measured KRN in four environments using a nested association mapping (NAM) population named HNAU-NAM1 with 1,617 recombinant inbred lines (RILs) that were derived from 12 maize inbred lines with a common parent, GEMS41. Then, five consensus quantitative trait loci (QTLs) distributing on four chromosomes were identified in at least three environments along with the best linear unbiased prediction (BLUP) values by the joint linkage mapping (JLM) method. These QTLs were further validated by the separate linkage mapping (SLM) and genome-wide association study (GWAS) methods. Three KRN genes cloned through the QTL assay were found in three of the five consensus QTLs, including qKRN1.1, qKRN2.1 and qKRN4.1. Two new QTLs of KRN, qKRN4.2 and qKRN9.1, were also identified. On the basis of public RNA-seq and genome annotation data, five genes highly expressed in ear tissue were considered candidate genes contributing to KRN. This study carried out a comprehensive analysis of the genetic architecture of KRN by using a new NAM population under multiple environments. The present results provide solid information for understanding the genetic components underlying KRN and candidate genes in qKRN4.2 and qKRN9.1. Single-nucleotide polymorphisms (SNPs) closely linked to qKRN4.2 and qKRN9.1 could be used to improve inbred yield during molecular breeding in maize.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The kernel row number (KRN) of an ear is an important trait related to yield and domestication in maize. Exploring the underlying genetic mechanisms of KRN has great research significance and ...application potential.
In the present study, N531 with a KRN of 18-22 and SLN with a KRN of 4-6 were used as the recurrent parent and the donor parent, respectively, to develop two introgression lines (ILs), IL_A and IL_B, both of which have common negative-effect alleles from SLN on chromosomes 1, 5 and 10 and significantly reduced inflorescence meristem (IM) diameter and KRN compared with those of N531. We used RNA-Seq to investigate the transcriptome profiles of 5-mm immature ears of N531, IL_A and IL_B. We identified a total of 2872 differentially expressed genes (DEGs) between N531 and IL_A, 2428 DEGs between N531 and IL_B and 1811 DEGs between IL_A and IL_B. A total of 1252 DEGs were detected as overlapping DEGs, and 89 DEGs were located on the common introgression fragments. Furthermore, three DEGs (Zm00001d013277, Zm00001d015310 and Zm00001d015377) containing three SNPs associated with KRN were identified using regional association mapping.
These results will facilitate our understanding of ear development and provide important candidate genes for further study on KRN.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Lower Cretaceous syn-orogenic sediments derived from the obducted ophiolites of the Meliata–Maliac–Vardar (Neotethys) Ocean are typically found in the Dinarides and the Austroalpine units. ...Correlative flysch-type deposits linking both regions through the Southern Alps had been reported from the Bohinj area (NW Slovenia), but their stratigraphic and structural framework remained poorly known. Our research focused on stratigraphic and structural field studies in a 50 km
2
area between Lake Bled and Lake Bohinj in the Julian Alps. The mixed carbonate–siliciclastic sediments, informally named the Studor formation, range in age from the Valanginian (possibly late Berriasian) to the Aptian. They occur on top of two different stratigraphic successions, which we assign to two separate nappes. The first succession consists of deep-water Middle Triassic to Lower Cretaceous deposits of the Bled Basin and belongs to the Pokljuka Nappe, which is the uppermost nappe of the Julian nappe stack. The second succession consists of Upper Triassic to Lower Jurassic platform carbonates and a thin Jurassic–Cretaceous deep-water sequence. This succession was deposited in the marginal area of the Julian Carbonate Platform/Julian High and now belongs to the underlying Krn Nappe. The original (Dinaric) thrust contacts between the Pokljuka and Krn nappes are obliterated by younger deformations. The present-day boundaries between these two nappes are steep NE–SW and younger NW–SE trending faults. The post-nappe deformation sequence characterizing the Alps–Dinarides transition zone has been recognized: (1) Oligocene–Early Miocene NW–SE contraction; (2) Early–Middle Miocene extension; and (3) Late Miocene to recent inversion and transpression.
A key intermediate corresponding to a rare sugar framework has been synthesized, starting from d-xylose, an inexpensive carbohydrate. This approach gave access to new elaborated sugar moieties for ...structure–activity relationships in the KRN research.
Meristems are central to plant growth and development, yet evidence of directly manipulating this control to improve crop yield is scarce. Kernel row number (KRN) is an important agronomic trait that ...can directly affect maize (Zea mays L.) yield. However, this trait is difficult to select by phenotyping, since it is highly variable in the mixed genetic backgrounds in early selfing generations. This study sought to improve this trait by marker-assisted backcrossing (MABC) of a weak allele of FASCIATED EAR 2 that is known to affect inflorescence meristem size, but the effect of which on yield is unclear. All of the four introgressed tropical elite inbreds of different heterotic groups, which are homozygous for the fea2-1328 allele, had 2–5 more KRNs compared to their respective recurrent parents. Furthermore, one hybrid made from crosses between two introgressed parents also had KRN increases that resulted in up to 28% yield increase compared to the original hybrid across multiple yield trials. The novel negative effects of the pericentromeric fea2 and/or its linkage drag effect on plant height, seed weight, and ear length, which could prevent line improvement, were revealed in several genetic backgrounds. Integration of conventional phenotypic selection to overcome these undesirable effects was discussed. This is the first work to demonstrate the possibility to increase yield of maize varieties using a mutation in a meristem size regulator. The crossing, selection strategies, and recombinant lines in this work can be applied to other elite maize hybrids and provide a potentially straightforward, non-transgenic way to improve the yield of an existing variety by 8–28%.
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