Chromosomal Segments Research Articles

Genome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena

BackgroundThe BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes).ResultsMost of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A. sativa.ConclusionsThe study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.

How chromosomal inversions reorient the evolutionary process.

Inversions are structural mutations that reverse the sequence of a chromosome segment and reduce the effective rate of recombination in the heterozygous state. They play a major role in adaptation, as well as in other evolutionary processes such as speciation. Although inversions have been studied since the 1920s, they remain difficult to investigate because the reduced recombination conferred by them strengthens the effects of drift and hitchhiking, which in turn can obscure signatures of selection. Nonetheless, numerous inversions have been found to be under selection. Given recent advances in population genetic theory and empirical study, here we review how different mechanisms of selection affect the evolution of inversions. A key difference between inversions and other mutations, such as single nucleotide variants, is that the fitness of an inversion may be affected by a larger number of frequently interacting processes. This considerably complicates the analysis of the causes underlying the evolution of inversions. We discuss the extent to which these mechanisms can be disentangled, and by which approach.

Identification and validation of seed dormancy loci and candidate genes and construction of regulatory networks by WGCNA in maize introgression lines.

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10% and three QTLs under multiple environments. Two QTL loci were co-located between the other two genetic mapping methods. Using differential gene expression analyses at two stages of grain development, gene functional analysis of Arabidopsis mutants, and gene functional analysis in the QTL region, seventeen PHS QTL-linked candidate genes were identified, and their five molecular regulatory networks constructed. Based on the Arabidopsis T-DNA mutations, three candidate genes were shown to regulate for SD and PHS. Meanwhile, using RNA-seq of grain development, the weighted correlation network analysis (WGCNA) was performed, deducing five regulatory pathways and target genes that regulate PHS and SD. Based on the conjoint analysis of GWAS and WGCNA, four pathways, nine target proteins and target genes were revealed, most of which regulate cell wall metabolism, cell proliferation and seed dehydration tolerance. This has important theoretical and practical significance for elucidating the genetic basis of maize PHS and SD, as well as mining of genetic resources and genetic improvement of traits.

Abstract C004: Assessing local ancestry inference using different sequencing assays and depth of coverage

Abstract Introduction: Several studies have reported differences in mutational frequencies between different ancestral populations. For example, PTEN alterations and TMPRSS2-ERG fusions are less common in men with African ancestry. However, these studies have primarily relied on measurements of "global ancestry" and have not been able to ascertain which genomic regions contribute to the observed differences in mutational frequencies. Recent advancements in computational algorithms now enable the estimation of “local ancestry” whereby individual chromosomal segments can be assigned to a particular ancestral background. These tools have been primarily developed for deep whole-genome sequencing (WGS) and have not been optimized for different sequencing assays including ultra-low pass WGS (ULP-WGS), whole exome sequencing (WES), and SNP genotyping arrays. The goal of our study is to establish best practices for local ancestry inference across a diverse set of sequencing and genotyping assays. Methods: We procured WGS data from four ancestries through the 1000 Genomes Project (n=1,067) for local ancestry inference. ULP-WGS and WES (with on- and off-target coverage) were simulated from the full WGS data. Pseudo-array data was emulated by restricting to SNP sites on Affymetrix Genome-Wide Human SNP array 6.0. Each genotype was imputed by Eagle-Beagle (EB) or GLIMPSE2 (GL2), and local ancestry inference was performed using G-nomix using window sizes spanning from 0.2 to 16.0 centimorgans (cM). Accuracy was assessed by comparing local ancestry calls for each assay in a training set (n=1007) to a validation set (n=62). Results: Local ancestry estimation in ULP-WGS data achieved an accuracy exceeding 98% when utilizing GL2, even with the smallest window size of 0.2 cM and a minimum sequencing depth of 0.1x. To achieve similar accuracy of 98% in ULP-WGS with EB, a window size of 1.5 cM was needed for sequencing depths from 2 to 0.5x, with a larger window size of 4 cM required for a depth of 0.25x. Interestingly, such accuracy did not obtain at a depth of 0.1x. For WES with on-target sites and pseudo-array data, we utilized EB for imputation as it was more computationally efficient and accurate with larger window sizes compared to GL2. The accuracy of WES with on-target sites exceeded 90% utilizing 4.0 cM or larger window sizes, but no window size achieved 98% accuracy. Incorporating off-target regions in WES and employing GL2 enhanced the accuracy to 98% at a window size of 1.5 cM. Pseudo-array data with EB achieved an accuracy of 98% at 0.5 cM and thus was better than WES. Conclusions: Our results show that local ancestry can be accurately estimated in different sequencing and genotyping assays when the window size and imputation tool are appropriately selected. This work will facilitate the use of local ancestry inference in studies utilizing different genotyping assays. Ultimately, researchers understand the influence of local ancestral haplotypes on molecular features of cancer. Citation Format: Tomoki Motegi, Joshua D. Campbell. Assessing local ancestry inference using different sequencing assays and depth of coverage [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C004.

A t(14;18) Negative Nodal Diffuse Follicular Lymphoma with 1p36/TNFRSF14 LOH Detected by Cytogenomic Microarray Analysis

Abstract Introduction/Objective Among the already described variants of nodal follicular lymphoma (FL), there is a variant with diffuse growth pattern with a predilection to involve the inguinal lymph nodes and peculiar immunohistochemical and molecular characteristics. The diffuse growth pattern is manifested by the complete absence of follicles without a follicular/dendritic meshwork (negative CD21 and CD23). This variant was first described by Katzenberger in 2009. It is distinguished from other variants by CD23 expression, lack of t(14;18)/ IGH::BCL2 rearrangement, and chromosome segment 1p36 deletion or TNFRSF14 mutations. Methods/Case Report A 43-year-old Caucasian male presented with a lump in his left groin, noted by him after exercising and sought surgical opinion to rule out inguinal hernia. CT- scan of abdomen and pelvis showed a well circumscribed 4.3 cm lymph node in the left groin region. Histological analysis of the lesion depicted a lymph node with a predominantly diffuse and focally vaguely nodular proliferation effacing the architecture. Numerous centrocytes admixed with occasional centroblasts averaging <15/HPF. The neoplastic cells are positive for CD20, PAX5, CD10, BCL6, CD23 and BCL2, and are negative for CD5 and cyclin D1. The CD21 highlights few residual germinal centers at the periphery of the lymph node. The proliferative (Ki67+) index is approximately 30-40%. Flow cytometry demonstrates CD10 positive, kappa monoclonal B cell population (20% of total). FISH analysis was negative for both IgH/BCL2 t(14;18) rearrangement and TNFRSF14 (1p36) Deletion. However, cytogenomic microarray analysis (CMA) revealed genomic imbalances and copy neutral Loss of Heterozygosity over 1p36 in a mosaic state representing about 40% of the cells, which notably encompasses PRKC2, SKI, TNFRSF14, PRDM16, TP73 and PRL22 genes. The findings are consistent with a final diagnosis of diffuse follicular lymphoma variant, WHO grade 1-2 of 3. Results (if a Case Study enter NA) N/A Conclusion The copy neutral Loss of Heterozygosity of 1p36 region which contains TNFRSF14 gene was detected by CMA only. Undoubtedly, CMA results can play a pivotal role in identifying copy neutral Loss of Heterozygosity or small regions deletions or gains that can be missed by conventional cytogenetics and FISH studies and subsequently establishing diagnosis and prognostic stratification of hematologic neoplasms.

A QTL allele from wild soybean enhances protein content without reducing the oil content

Abstract Soybean is one of the chief crops producing protein and oil for human consumption. Wild soybean, the ancestor of cultivated soybean, possesses high seed protein content; therefore, it is a valuable genetic resource that could enhance protein content in the cultivated varieties. To identify the genes responsible for increasing protein content in wild soybean, a population comprising 113 BC4F6 chromosome segment substitution lines (CSSL) was developed from a cross between soybean cultivar ‘Jackson’ and wild soybean accession JWS156-1. The CSSL population was cultivated in the field conditions for 3 years (2018, 2019 and 2020), and the seeds harvested from each line were analysed for protein and oil contents by InfraTec Nova instrument. Quantitative trait locus (QTL) analysis with 243 SSR markers identified 12 QTLs associated with seed protein, oil and protein + oil contents. Among these QTLs, qPro8 and qPro19, two major and stable QTLs for protein content, were detected on chromosomes 8 and 19, respectively. No QTL for oil content was detected in the vicinity of qPro19, indicating that qPro19 did not influence the seed oil content. The effect of qPro19 was validated using near-isogenic lines (NILs) of qPro19. By introducing the qPro19 allele from wild soybean into another soybean variety, ‘Tachiyutaka’, a BC4 line, T-678, that showed enhanced seed protein content, without reducing the seed oil content. This study implied that the qPro19 allele from wild soybean could be a potential genetic resource for breeding programmes aimed to improve soybean seed quality.

Chromoanagenesis in Haematological Malignancy: Review of Samples from Patients with Acute Leukemia and MDS

Background: Complex chromosome rearrangements (CCRs) include a variety of structural aberrations grouped as chromothripsis, chromoanasynthesis and chromoplexy. Although the underlying mechanisms for these phenomena are unknown and likely to be different, they appear to originate from a single event. While chromothripsis and chromoanasynthesis affect limited genome sites their role and genome associations in haematological malignancy remain to be elucidated. Aims: This study aimed to provide clarity on the location, incidence and association with TP53 gene profile of chromothripsis (cth) and chromoanasynthesis (cha) events in MDS/AML. Methods: We analysed data from routine investigations carried out by haematological malignancy diagnostic service (HMDS) at University College London Hospital (UCLH) on 2,506 samples of acute myeloid leukaemia (AML) and myelodysplasia (MDS), including G-banding, FISH (Cytocell), chromosome microarray analysis (CMA, Agilent) and target NGS(Illumina). Analysis of 87 samples with complex bone marrow karyotypes were reported following the ISCN 2020 as: (i) cth(alternating disomy and heterozygous loss along a chromosome or chromosomal segment) or (ii) cha (deletions and one or two copy number gains in a single chromosome or chromosome region including copy number variants without the clustered breakpoints of chromothripsis). Statistical analysis used RStudio (v 1.4.1106) to carry Pearson's chi-squared (χ²) and Fisher's exact (2-sided) tests. Results: Complex karyotypes harbouring cth and cha type aberrations were detected in 65 out of 727 AML and 22 out of 1779 MDS samples. The cth events were seen alongside cha in 67% of cases, rarely presenting as a sole abnormality (2%), while cha alone was found in 31% of samples. Most frequently cth was mapped at chromosome 21 (17%), chromosome 7 (15%), chromosome 17 and 19 (13%) and chromosome 5 (11%) (Fig.1a). In this cohort of 87cases, chromothripsis was found to be associated with TP53 deletions ( TP53Del/WT) in 7 (7%) and with TP53 mutations ( TP53Dpl/mut) in 22 (25%), while concurrent TP53 deletions and mutations ( TP53Del/mut) were detected in 29 (33%) ( p = 0.0005). Samples with TP53Del/mut harboured cth in chromosomes 7 (7%), 17 (6%), 8, 9, 19 and 21 (5%) whilst cases with TP53Dpl/mut had cth in chromosomes 21 (9%), 19 (8%), 5 (7%) and 7 (5%). (Fig 1 b). The cha aberrations generally followed the genome location of cth events with some exception. Firstly, chromosomes X,13 and 21 appear to have only cth and is seen at slightly higher level on chromosome 19 (cth 13% vs cha 9%). Secondly, cha was most frequently seen on 5q (61 %), chromosome 17 (40%) and 7q (34%). However, the same chromosomes also had the greatest number of cases presenting with concurrent cth and cha, seen in 63/87 (72%) for chromosome 5, 46/87 (53%) for chromosome 17 and 43/87 (49%) for chromosome 7. Importantly, only cases harbouring 5q deletions showed a statistically significant association with TP53 status ( p = 0.0011) in this cohort irrespective of cth and cha presence. Notably, 24/29 cases (83%) with TP53Del/mut were cth positive and had 5q31 deletion. This finding is an important observation but not in keeping with reports of exclusive association of TP53 mutations with concurrent 5q and 7q loss (1, 2 and 3). The concurrent recording of cth and cha performed by this study could explain the discrepancy, most likely due to high frequency of cha events in 5q. Summary This study highlights issues pertinent to risk stratification in routine diagnostic settings: (i) MDS/AML cases with complex genome harbouring either or both cth and cha share common TP53 aberrations (del/mut) and (ii) deletion of 5q31 is positively associated with TP53 aberrations and presence of cth events. (iii) CMA offers a comprehensive, sensitive, fast and financially superior way to detect cth, cha events along with genome complexity compared to G banding complemented by FISH. Overall, combining CMA and TP53 mutation screening offers a fast, reliable way to detect high risk disease in MDS/AML. Keywords: Complex genome, CMA, chromothripsis, TP53 mutations

Effect of yeast chromosome II aneuploidy on malate production in sake brewing

Chromosome aneuploidy is a common phenomenon in industrial yeast. Aneuploidy is considered one of the strategies to enhance the industrial properties of Saccharomyces cerevisiae strains. However, the effects of chromosomal aneuploidy on the brewing properties of sake have not been extensively studied. In this study, sake brewing was performed using a series of genome-wide segmental duplicated laboratory S.cerevisiae strains, and the effects of each segmentally duplicated region on sake brewing were investigated. We found that the duplication of specific chromosomal regions affected the production of organic acids and aromatic compounds in sake brewing. As organic acids significantly influence the taste of sake, we focused on the segmental duplication of chromosome II that alters malate levels. Sake yeast Kyokai No. 901 strains with segmental chromosome II duplication were constructed using a polymerase chain reaction-mediated chromosomal duplication method, and sake was brewed using the resultant aneuploid sake yeast strains. The results showed the possibility of developing sake yeast strains exhibiting low malate production without affecting ethanol production capacity. Our study revealed that aneuploidy in yeast alters the brewing properties; in particular, the aneuploidy of chromosome II alters malate production in sake brewing. In conclusion, aneuploidization can be a novel and useful tool to breed sake yeast strains with improved traits, possessing industrial significance.

An Integral R-Banded Karyotype Analysis System of Bone Marrow Metaphases Based on Deep Learning.

Conventional karyotype analysis, which provides comprehensive cytogenetic information, plays a significant role in the diagnosis and risk stratification of hematologic neoplasms. The main limitations of this approach include long turnaround time and laboriousness. Therefore, we developed an integral R-banded karyotype analysis system for bone marrow metaphases, based on deep learning. To evaluate the performance of the internal models and the entire karyotype analysis system for R-banded bone marrow metaphase. A total of 4442 sets of R-banded normal bone marrow metaphases and karyograms were collected. Accordingly, 4 deep learning-based models for different analytic stages of karyotyping, including denoising, segmentation, classification, and polarity recognition, were developed and integrated as an R-banded bone marrow karyotype analysis system. Five-fold cross validation was performed on each model. The whole system was implemented by 2 strategies of automatic and semiautomatic workflows. A test set of 885 metaphases was used to assess the entire system. The denoising model achieved an intersection-over-union (IoU) of 99.20% and a Dice similarity coefficient (DSC) of 99.58% for metaphase acquisition. The segmentation model achieved an IoU of 91.95% and a DSC of 95.79% for chromosome segmentation. The accuracies of the segmentation, classification, and polarity recognition models were 96.77%, 98.77%, and 99.93%, respectively. The whole system achieved an accuracy of 93.33% with the automatic strategy and an accuracy of 99.06% with the semiautomatic strategy. The performance of both the internal models and the entire system is desirable. This deep learning-based karyotype analysis system has potential in a clinical application.

116 Using Theoretical and Realized Accuracies to Estimate Changes in Heritabilities

Abstract Under genomic selection, heritabilities for strongly selected traits are reduced, and antagonism between production and fitness traits can intensify. However, estimating genetic parameters by established methods such as REML or Bayesian with large genomic data is computationally expensive or unfeasible. In this study, we investigated the use of theoretical and realized accuracies to estimate heritabilities. The first dataset for pigs included 161k phenotypic records for a growth trait (GT), 27k phenotypic records for a fitness trait (FT), and 55k animals were genotyped. The second dataset for broilers contained 820K phenotypes for a growth trait (GT), and 154k animals were genotyped. Theoretical accuracies (r) were calculated as r = sqrt(Nh2/(Nh2+Me)) assuming the number of independent chromosome segments (Me) of 5k and the number of observations (N) equal to the number of genotypes or phenotypes, whichever was smaller. Estimated accuracies were calculated by the linear regression (LR) method. Assumed heritabilities were recent estimates for pigs (0.21 for GT and 0.04 for FT) and an older estimate for broilers (0.30). For the pig dataset, the theoretical and realized accuracies were similar: 0.82 and 0.84 for GT, and 0.42 and 0.43 for FT, suggesting that the assumed heritabilities were realistic. For the broiler dataset, the theoretical and realized accuracies differed: 0.94 and 0.56, indicating possible large differences between real and assumed heritabilities. Both accuracies could be made equal at 0.89 by assuming a heritability of 0.13. Such a heritability was also found to provide a realistic estimate of the genetic gain with recent data. Comparisons of theoretical and realized accuracies may be used as a tool to estimate changing heritabilities over successive generations at a low cost. Similar formulas may enable low-cost estimation of genetic correlations.

GENETIC ENHANCEMENT OF SOYBEAN (GLYCINE MAX L.) GERMPLASM FOR ADAPTABILITY AND PRODUCTIVITY

Soybean is an essential protein and oilseed crop, but environmental factors, such as photoperiod and altitude, highly influence its growth. Poor adaptability of soybean cultivars may result in a significant decrease in seed yield due to disruption of flowering or maturity. It is, therefore, vital to select cultivars adapted to specific regions of the world. Global climate change, causing increasing temperature and associated water deficit stress, may further challenge sustainable soybean production worldwide. Therefore, it is necessary to understand genetic responses in soybeans induced by environmental variables. This review highlights previous research showing how several quantitative trait loci (QTLs) activated by photo-thermal responses affected soybean flowering. We discuss cytogenetic stocks, including chromosome segment substitution lines, and their role in introgressing novel genes from wild soybeans. A review of genes showing responses to various environmental variables that affect soybean adaptability is also ensued, with putative functions suggested. These include gene response regulation to temperature and heat stress, identified via genetic mapping, and emerged as tools for developing adapted soybean cultivars.

100 Pedigree Effective Population Size Affects Genomic Prediction Accuracy in Katahdin Sheep

Abstract Katahdin sheep are a composite hair breed of medium-size, relatively prolific, with potential to exhibit resistance to gastrointestinal parasites. Recently, genomic predictions of breeding values were introduced in Katahdins. Prediction accuracy depends on the genetic variation present, and selection using genomically-enhanced breeding values may reduce diversity. We aimed to characterize the current genetic variability in Katahdins utilizing their extensive pedigree. The National Sheep Improvement Program provided the pedigree of 92,030 sheep born from 1984-2019. Two reference populations were defined for animals born between 2017-2019: all Katahdins (n = 23,494), and Katahdins with at least three generations of known Katahdin ancestry (n = 9,327). Using ENDOG and PopReport, effective population sizes (Ne) were estimated. We then considered the effect of Ne on the size of the genomic reference population needed to achieve certain levels of prediction accuracy. Weaning weight, a lowly heritable trait for this breed (h2 = 0.13), was evaluated. Based on individual increase in inbreeding, inbreeding coefficient of animal adjusted for equivalent complete generations, the estimated Ne for the full pedigree, reference 1, and reference 2 were 92, 104, and 87, respectively. When inbreeding coefficients were regressed or log-regressed on birth date and adjusted for generation interval, the Ne estimates were 53 and 49 for reference 1, and 76 and 67 for reference 2, respectively. For our average Ne = 75 with 3,960 effective chromosomal segments, the accuracy of prediction for weaning weight was estimated for genomic reference population sizes (N) of 10k, 15k, 20k, and 25k. Starting at N = 10k, the prediction accuracy was 0.58, and as N increased by 5k increments the accuracy increased to 0.65, 0.70, and 0.74. Conversely, with our smallest Ne = 49 with 2,548 effective chromosomal segments, the prediction accuracy was 0.64, 0.71, 0.75, and 0.78 for N = 10k, 15k, 20k, and 25k, respectively. Estimated Ne varied depending on the method utilized, and tended to be larger for reference 1 than 2. However, this was not the case for Ne based on regression. Inbreeding coefficients were greater in reference 2 than 1, and the generation interval was shorter in reference 2 (2.84 years) than in 1 (2.97 years). These combined differences led to larger Ne estimates for reference 2 than 1, reflecting the impact of different criteria used to obtain this statistic. The generally small, estimated Ne benefitted genomic prediction due to a greater shared number of effective chromosomal segments. Investing in larger genomic reference populations will only marginally increase prediction accuracy even for lowly heritable traits. Selection using genomically-enhanced breeding values will accelerate genetic gains, potentially reducing the Ne of Katahdins and thereby increasing prediction accuracy. Yet, long-term gains may be at risk due to the loss of genetic diversity.

Identification and introgression of a novel leaf rust resistance gene from Thinopyrum intermedium chromosome 7Js into wheat.

A novel leaf rust resistance locus located on a terminal segment (0-69.29 Mb) of Thinopyrum intermedium chromosome arm 7JsS has been introduced into wheat genome for disease resistance breeding. Xiaoyan 78829, a wheat-Thinopyrum intermedium partial amphiploid, exhibits excellent resistance to fungal diseases in wheat. To transfer its disease resistance to common wheat (Triticum aestivum), we previously developed a translocation line WTT26 using chromosome engineering. Disease evaluation showed that WTT26 was nearly immune to 14 common races of leaf rust pathogen (Puccinia triticina) and highly resistant to Ug99 race PTKST of stem rust pathogen (P. graminis f. sp. tritici) at the seedling stage. It also displayed high adult plant resistance to powdery mildew (caused by Blumeria graminis f. sp. tritici). Cytogenetic and molecular marker analysis revealed that WTT26 carried a T4BS·7JsS chromosome translocation. Once transferred into the susceptible wheat genetic background, chromosome 7JsS exhibited its resistance to leaf rust, indicating that the resistance locus was located on this alien chromosome. To enhance the usefulness of this locus in wheat breeding, we further developed several new translocation lines with small Th. intermedium segments using irradiation and developed 124 specific markers using specific-locus amplified fragment sequencing, which increased the marker density of chromosome 7JsS. Furthermore, a refined physical map of chromosome 7JsS was constructed with 74 specific markers, and six bins were thus arranged according to the co-occurrence of markers and alien chromosome segments. Combining data from specific marker amplification and resistance evaluation, we mapped a new leaf rust resistance locus in the 0-69.29Mb region on chromosome 7JsS. The translocation lines carrying the new leaf rust resistance locus and its linked markers will contribute to wheat disease-resistance breeding.

Neuroblastoma Patients' Outcome and Chromosomal Instability.

Chromosomal instability (CIN) induces a high rate of losses or gains of whole chromosomes or parts of chromosomes. It is a hallmark of most human cancers and one of the causes of aneuploidy and intra-tumor heterogeneity. The present study aimed to evaluate the potential prognostic role of CIN in NB patients at diagnosis. We performed array comparative genomic hybridization analyses on 451 primary NB patients at the onset of the disease. To assess global chromosomal instability with high precision, we focused on the total number of DNA breakpoints of gains or losses of chromosome arms. For each tumor, an array-CGH-based breakpoint instability index (BPI) was assigned which defined the total number of chromosomal breakpoints per genome. This approach allowed us to quantify CIN related to whole genome disruption in all NB cases analyzed. We found differences in chromosomal breakages among the NB clinical risk groups. High BPI values are negatively associated with survival of NB patients. This association remains significant when correcting for stage, age, and MYCN status in the Cox model. Stratified analysis confirms the prognostic effect of BPI index in low-risk NB patients with non-amplified MYCN and with segmental chromosome aberrations.

The genome of Salmacisia buchloëana, the parasitic puppet master pulling strings of sexual phenotypic monstrosities in buffalograss.

To complete its parasitic lifecycle, Salmacisia buchloëana, a biotrophic fungus, manipulates reproductive organ development, meristem determinacy, and resource allocation in its dioecious plant host, buffalograss (Bouteloua dactyloides; Poaceae). To gain insight into S. buchloëana's ability to manipulate its host, we sequenced and assembled the 20.1 Mb genome of S. buchloëana into 22 chromosome-level pseudomolecules. Phylogenetic analysis suggests that S. buchloëana is nested within the genus Tilletia and diverged from Tilletia caries and Tilletia walkeri ∼40 MYA. We find that S. buchloëana contains a novel chromosome arm with no syntenic relationship to other publicly available Tilletia genomes, and that genes on the novel arm are upregulated upon infection, suggesting that this unique chromosomal segment may have played a critical role in S. buchloëana's evolution and host specificity. Salmacisia buchloëana has one of the largest fractions of serine peptidases (1.53% of the proteome) and one of the highest GC contents (62.3%) in all classified fungi. Analysis of codon base composition indicated that GC content is controlled more by selective constraints than directional mutation, and that S. buchloëana has a unique bias for the serine codon UCG. Finally, we identify 3 inteins within the S. buchloëana genome, 2 of which are located in a gene often used in fungal taxonomy. The genomic and transcriptomic resources generated here will aid plant pathologists and breeders by providing insight into the extracellular components contributing to sex determination in dioecious grasses.

Identification of a Seed Vigor–Related QTL Cluster Associated with Weed Competitive Ability in Direct–Seeded Rice (Oryza Sativa L.)

Direct seeding of rice (Oryza sativa L.) is a low-labor and sustainable cultivation method that is used worldwide. Seed vigor and early vigor are important traits associated with seedling stand density (SSD) and weed competitive ability (WCA), which are key factors in direct-seeded rice (DSR) cultivation systems. Here, we developed a set of chromosome segment substitution lines with Xiushui134 as receptor parent and Yangdao6 as donor parent and used these lines as a mapping population to identify quantitative trait loci (QTLs) for seed vigor, which we evaluated based on germinability–related indicators (germination percentage (GP), germination energy (GE), and germination index (GI)) and seedling vigor–related indicators (root number (RN), root length (RL), and shoot length (SL) at 14 days after imbibition) under controlled conditions in an incubator. Ten QTLs were detected across four chromosomes, of which a cluster of QTLs (qGP11, qGE11, qGI11, and qRL11) co-localized on Chr. 11 with high LOD values (12.03, 8.13, 7.14, and 8.75, respectively). Fine mapping narrowed down the QTL cluster to a 0.7-Mb interval between RM26797 and RM6680. Further analysis showed that the QTL cluster has a significant effect (p < 0.01) on early vigor under hydroponic culture (root length, total dry weight) and direct seeding conditions (tiller number, aboveground dry weight). Thus, our combined analysis revealed that the QTL cluster influenced both seed vigor and early vigor. Identifying favorable alleles at this QTL cluster could facilitate the improvement of SSD and WCA, thereby addressing both major factors in DSR cultivation systems.

Transcriptome analysis reveals ZmERF055 contributes to waterlogging tolerance in sweetcorn

Waterlogging is a major disaster damaging crop production. However, most sweetcorn cultivars are not tolerant to waterlogging, which severely threatens their production. In order to understand the genetic mechanisms underlying waterlogging tolerance in sweetcorn, this study conducted a comprehensive investigation of sweetcorn waterlogging tolerance at the levels of physiology, biochemistry, and transcriptome in two sweetcorn CSSLs (chromosome segment substitution lines), D120 and D81. We found that D120 showed increased plant height, root length, root area, adventitious root numbers, antioxidant enzyme activities, and aerenchyma area ratio compared to D81. The transcriptome results showed that 2492 and 2351 differentially expressed genes (DEGs) were obtained at 4 h and 8 h of waterlogging treatment, respectively. Genes involved in reactive oxygen species (ROS) homeostasis, photosynthesis, and alcohol fermentation are sensitive in the waterlogging tolerant genotype D120, resulting in enhanced ROS scavenging ability, adventitious roots, and aerenchyma formation. Additionally, ethylene-, auxin-, and ABA-related genes exhibited different responses to waterlogging stress in sweetcorn. We integrated transcriptome and differential chromosomal fragments data and identified that ZmERF055 on chromosome 9 was directly involved in waterlogging stress. ZmERF055-overexpressing plants consistently exhibited significantly increased waterlogging tolerance and ROS homeostasis in Arabidopsis. These results offer a network of plant hormone signaling, ROS homeostasis, and energy metabolism co-modulating waterlogging tolerance in sweetcorn. Additionally, the findings support ZmERF055 as a potential ideal target gene in crop breeding to improve plant waterlogging tolerance.

Meta-Analysis and Multiomics of a Chromosome Segment Substitution Line Reveal Candidate Genes Associated with Seed Hardness in Soybean.

Soybean seed hardness is a key trait that influences planting, nutritional quality, and postharvest processing, but its genetic and molecular mechanisms remain to be clarified. We used meta-analysis to detect 17 meta-quantitative trait locus (QTLs) for soybean seed hardness. We then identified a hard-seeded chromosome segment substitution line, R75, with fragments introduced from hard-seeded wild germplasm in four of the meta-QTL intervals. Observations of the seed coat ultrastructure revealed thicker palisade tissue in R75 than in its soft-seeded recurrent parent. Transcriptomics and proteomics of R75 and its recurrent parent revealed multiple candidate genes associated with seed hardness. Fifty-seven were located on homozygous introduced fragments, 26 in meta-QTL intervals, and one in both (Glyma.02G268600). Five initial candidates were selected for KASP marker development on the basis of their predicted functions and nonsynonymous SNPs. The selection efficiency of the markers was as high as 90% for nonhard lines and 43% for hard lines in the chromosome segment substitution line (CSSL) population.

A 4.43-Kb deletion of chromosomal segment containing an ovate family protein confers long capsule in sesame (Sesamum indicum L.).

A 4.43-Kb structural variation in the sesame genome results in the deletion of the Siofp1 gene and induces the long capsule length trait. Capsule length (CL) has a positive effect on seed weight and yield in various agronomically important species; however, the molecular mechanism underlying long capsule trait regulation in sesame remains unknown. The inheritance analysis showed that long capsule traits (CL > 4.0cm) were dominant over normal length (average CL = 3.0cm) and were controlled by a single gene pair. Association mapping with a RIL population and 259 natural sesame germplasm accessions indicated that the target interval was 52,830-730,961bp of SiChr.10 in sesame. Meanwhile, the structural variation (SV) of the association mapping revealed that only SV_414325 on chromosome 10 was significantly associated with the CL trait, with a P value of 1.1135E-19. SV_414325 represents a 4430-bp deletion from 414,325 to 418,756bp on SiChr.10, covering Sindi_2155000 (named SiOFP1). In the normal length type, Siofp1 encodes 411 amino acids of the ovate family proteins and is highly expressed in the leaf, stem, bud, and capsule tissues of sesame. In accordance with the transcriptional repressor character, Siofp1 overexpression in transgenic Arabidopsis (T0 and T1 generations) induced a 25-39% greater shortening of silique length than the wild type (P < 0.05), as well as round cauline leaves and short carpels. These results confirm that SiOFP1 plays a key role in regulating CL trait in sesame and other flowering plants. These findings provide a theoretical and material basis for sesame capsule development and high-yield breeding research.

Genomic introgressions from African rice (Oryza glaberrima) in Asian rice (O. sativa) lead to the identification of key QTLs for panicle architecture

BackgroundDeveloping high yielding varieties is a major challenge for breeders tackling the challenges of climate change in agriculture. The panicle (inflorescence) architecture of rice is one of the key components of yield potential and displays high inter- and intra-specific variability. The genus Oryza features two different crop species: Asian rice (Oryza sativa L.) and the African rice (O. glaberrima Steud.). One of the main morphological differences between the two independently domesticated species is the structure (or complexity) of the panicle, with O. sativa displaying a highly branched panicle, which in turn produces a larger number of grains than that of O. glaberrima. The gene regulatory network that governs intra- and interspecific panicle diversity is still under-studied.ResultsTo identify genetic factors linked to panicle architecture diversity in the two species, we used a set of 60 Chromosome Segment Substitution Lines (CSSLs) issued from third generation backcross (BC3DH) and carrying genomic segments from O. glaberrima cv. MG12 in the genetic background of O. sativa Tropical Japonica cv. Caiapó. Phenotypic data were collected for rachis and primary branch length, primary, secondary and tertiary branch number and spikelet number. A total of 15 QTLs were localized on chromosomes 1, 2, 3, 7, 11 and 12, QTLs associated with enhanced secondary and tertiary branch numbers were detected in two CSSLs. Furthermore, BC4F3:5 lines carrying different combinations of substituted segments were produced to decipher the effects of the identified QTL regions on variations in panicle architecture. A detailed analysis of phenotypes versus genotypes was carried out between the two parental genomes within these regions in order to understand how O. glaberrima introgression events may lead to alterations in panicle traits.ConclusionOur analysis led to the detection of genomic variations between O. sativa cv. Caiapó and O. glaberrima cv. MG12 in regions associated with enhanced panicle traits in specific CSSLs. These regions contain a number of key genes that regulate panicle development in O. sativa and their interspecific genomic variations may explain the phenotypic effects observed.