Artificial Selection Research Articles

Uncovering the genetic architecture of parallel evolution.

Identifying the genetic architecture underlying adaptive traits is exceptionally challenging in natural populations. This is because associations between traits not only mask the targets of selection but also create correlated patterns of genomic divergence that hinder our ability to isolate causal genetic effects. Here, we examine the repeated evolution of components of the auxin pathway that have contributed to the replicated loss of gravitropism (i.e. the ability of a plant to bend in response to gravity) in multiple populations of the Senecio lautus species complex in Australia. We use a powerful approach which combines parallel population genomics with association mapping in a Multiparent Advanced Generation Inter-Cross (MAGIC) population to break down genetic and trait correlations to reveal how adaptive traits evolve during replicated evolution. We sequenced auxin and shoot gravitropism-related gene regions in 80 individuals from six natural populations (three parallel divergence events) and 133 individuals from a MAGIC population derived from two of the recently diverged natural populations. We show that artificial tail selection on gravitropism in the MAGIC population recreates patterns of parallel divergence in the auxin pathway in the natural populations. We reveal a set of 55 auxin gene regions that have evolved repeatedly during the evolution of the species, of which 50 are directly associated with gravitropism divergence in the MAGIC population. Our work creates a strong link between patterns of genomic divergence and trait variation contributing to replicated evolution by natural selection, paving the way to understand the origin and maintenance of adaptations in natural populations.

Functional allele of a MATE gene selected during domestication modulates seed color in chickpea.

Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.

Genome assembly of KA105, a new resource for maize molecular breeding and genomic research

Superior inbred lines are central to maize breeding as sources of natural variation. Although many elite lines have been sequenced, less sequencing attention has been paid to newly developed lines. We constructed a genome assembly of the elite inbred line KA105, which has recently been developed by an artificial breeding population named Shaan A and has shown desirable characteristics for breeding. Its pedigree showed genetic divergence from B73 and other lines in its pedigree. Comparison with the B73 reference genome revealed extensive structural variation, 58 presence/absence variation (PAV) genes, and 1023 expanded gene families, some of which may be associated with disease resistance. A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes, of which eight were induced by at least one kind of stress, participating in gene modules responding to stress such as drought and southern leaf blight disease. More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development. The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

A terpene synthase supergene locus determines chemotype in Melaleuca alternifolia (tea tree).

Leaf oil terpenes vary categorically in many plant populations, leading to discrete phenotypes of adaptive and economic significance, but for most species, a genetic explanation for the concerted fluctuation in terpene chemistry remains unresolved. To uncover the genetic architecture underlying multi-component terpene chemotypes in Melaleuca alternifolia (tea tree), a genome-wide association study was undertaken for 148 individuals representing all six recognised chemotypes. A number of single nucleotide polymorphisms in a genomic region of c. 400 kb explained large proportions of the variation in key monoterpenes of tea tree oil. The region contained a cluster of 10 monoterpene synthase genes, including four genes predicted to encode synthases for 1,8-cineole, terpinolene, and the terpinen-4-ol precursor, sabinene hydrate. Chemotype-dependent null alleles at some sites suggested structural variants within this gene cluster, providing a possible basis for linkage disequilibrium in this region. Genotyping in a separate domesticated population revealed that all alleles surrounding this gene cluster were fixed after artificial selection for a single chemotype. These observations indicate that a supergene accounts for chemotypes in M. alternifolia. A genetic model with three haplotypes, encompassing the four characterised monoterpene synthase genes, explained the six terpene chemotypes, and was consistent with available biparental cross-segregation data.

Genetic Distinctness and Diversity of American Aberdeen Cattle Compared to Common Beef Breeds in the United States.

American Aberdeen (AD) cattle in the USA descend from an Aberdeen Angus herd originally brought to the Trangie Agricultural Research Centre, New South Wales, AUS. Although put under specific selection pressure for yearling growth rate, AD remain genomically uncharacterized. The objective was to characterize the genetic diversity and structure of purebred and crossbred AD cattle relative to seven common USA beef breeds using available whole-genome SNP data. A total of 1140 animals consisting of 404 purebred (n = 8 types) and 736 admixed individuals (n = 10 types) was used. Genetic diversity metrics, an analysis of molecular variance, and a discriminant analysis of principal components were employed. When linkage disequilibrium was not accounted for, markers influenced basic diversity parameter estimates, especially for AD cattle. Even so, intrapopulation and interpopulation estimates separate AD cattle from other purebred types (e.g., Latter's pairwise FST ranged from 0.1129 to 0.2209), where AD cattle were less heterozygous and had lower allelic richness than other purebred types. The admixed AD-influenced cattle were intermediate to other admixed types for similar parameters. The diversity metrics separation and differences support strong artificial selection pressures during and after AD breed development, shaping the evolution of the breed and making them genomically distinct from similar breeds.

Sterilized Anopheles funestus can autodisseminate sufficient pyriproxyfen to the breeding habitat under semi-field settings

BackgroundAnopheles funestus, the main malaria vector, prefer to oviposit in permanent and/or semi-permanent breeding habitats located far from human dwellings. Difficulties in identifying and accessing these habitats jeopardize the feasibility of conventional larviciding. In this way, a semi-field study was conducted to assess the potential of autodissemination of pyriproxyfen (PPF) by An. funestus for its control.MethodsThe study was conducted inside a semi-field system (SFS). Therein, two identical separate chambers, the treatment chamber with a PPF-treated clay pot (0.25 g AI), and the control chamber with an untreated clay pot. In both chambers, one artificial breeding habitat made of a plastic basin with one litre of water was provided. Three hundred blood-fed female An. funestus aged 5–9 days were held inside untreated and treated clay pots for 30 min and 48 h before being released for oviposition. The impact of PPF on adult emergence, fecundity, and fertility through autodissemination and sterilization effects were assessed by comparing the treatment with its appropriate control group.ResultsMean (95% CI) percentage of adult emergence was 15.5% (14.9–16.1%) and 70.3% (69–71%) in the PPF and control chamber for females exposed for 30 min (p < 0.001); and 19% (12–28%) and 95% (88–98%) in the PPF and control chamber for females exposed for 48 h (p < 0.001) respectively. Eggs laid by exposed mosquitoes and their hatch rate were significantly reduced compared to unexposed mosquitoes (p < 0.001). Approximately, 90% of females exposed for 48 h retained abnormal ovarian follicles and only 42% in females exposed for 30 min.ConclusionThe study demonstrated sterilization and adult emergence inhibition via autodissemination of PPF by An. funestus. Also, it offers proof that sterilized An. funestus can transfer PPF to prevent adult emergence at breeding habitats. These findings warrant further assessment of the autodissemination of PPF in controlling wild population of An. funestus, and highlights its potential for complementing long-lasting insecticidal nets.

Genome Variation Map of Domestic Qinghai-Tibet Plateau Yaks by SLAF-Seq Reveals Genetic Footprint during Artificial Selection.

The yak (Bos grunniens) was domesticated in the high-altitude QTP. Research about their genetic diversity and population structure is limited. In this study, we resequenced the genome of 494 domestic yaks using Specific-Locus Amplified Fragment Sequencing (SLAF-seq). The survey was conducted on six populations sampled from isolated locations in China in order to analyze their structure and genetic diversity. These six domestic populations were clearly grouped into two independent clusters, with Jinchuan, Changtai, and Jiulong showing a tight genetic relationship with the wild yak. Nerve development pathways were enriched with GO enrichment analysis of 334 domesticated genes. Major genomic regions associated with the differentiation of domestic yaks were detected. These findings provide preliminary information on the yak genome variability, useful to understand the genomic characteristics of different populations in QTP.

Genomic selection analysis of morphological and adaptation traits in Chinese indigenous dog breeds.

The significant morphological differences and abundant germplasm resources of Chinese indigenous dog breeds can be attributed to the diverse geographical environment, including plateaus, mountains, and a long history of raising dogs. The combination of both natural and artificial selection during the past several thousand years has led to hundreds of dog breeds with distinct morphological traits and environmental adaptations. China is one of the earliest countries to domesticate dogs and there are more than 50 ancient indigenous dog breeds. In this study, the run of homozygosity (ROH) and proportion of the autosomal genome covered by ROHs (FROH) were calculated for 10 dog breeds that are the most representative Chinese indigenous dogs based on 170K SNP microarray. The results of FROH showed that the Chuandong hound dogs (HCSSC) have the highest level of inbreeding among the tested breeds. The inbreeding in HCSSC occurred more recently than the Liangshan dogs (SCLSQ) dogs because of more numbers of long ROHs in HCSSC dogs, and the former also have higher inbreeding degree. In addition, there are significant differences in the inbreeding degree among different subpopulations of the same breed, such as the Thin dogs from Shaanxi and Shandong province. To explore genome-wide selection signatures among different breeds, including coat color, ear shape, and altitude adaptability, we performed genome selection analyses of FST and cross population extended haplotype homozygosity (XP-EHH). For the coat color, the FST analysis between Xiasi dogs (XSGZ) and HCSSC dogs was performed and identified multiple genes involved in coat color, hair follicle, and bone development, including MC1R, KITLG, SOX5, RSPO2, and TBX15. For the plateau adaptability, we performed FST and XP-EHH analyses between dogs from Tibet (Tibetan Mastiffs and Nyingchi dogs) and plain regions (Guangxi Biwei dogs GXBWQ and Guandong Sharpei dogs). The results showed the EPAS1 gene in dogs from Tibet undergo strong selection. Multiple genes identified for selection signals based on different usage of dogs. Furthermore, the results of ear shape analyses showed that MSRB3 was likely to be the main gene causing the drop ear of domestic dogs. Our study provides new insights into further understanding of Chinese indigenous dogs.

Analysis of polygenic selection in purebred and crossbred pig genomes using generation proxy selection mapping

BackgroundArtificial selection on quantitative traits using breeding values and selection indices in commercial livestock breeding populations causes changes in allele frequency over time at hundreds or thousands of causal loci and the surrounding genomic regions. In population genetics, this type of selection is called polygenic selection. Researchers and managers of pig breeding programs are motivated to understand the genetic basis of phenotypic diversity across genetic lines, breeds, and populations using selection mapping analyses. Here, we applied generation proxy selection mapping (GPSM), a genome-wide association analysis of single nucleotide polymorphism (SNP) genotypes (38,294–46,458 markers) of birth date, in four pig populations (15,457, 15,772, 16,595 and 8447 pigs per population) to identify loci responding to artificial selection over a period of five to ten years. Gene-drop simulation analyses were conducted to provide context for the GPSM results. Selected loci within and across each population of pigs were compared in the context of swine breeding objectives.ResultsThe GPSM identified 49 to 854 loci as under selection (Q-values less than 0.10) across 15 subsets of pigs based on combinations of populations. The number of significant associations increased when data were pooled across populations. In addition, several significant associations were identified in more than one population. These results indicate concurrent selection objectives, similar genetic architectures, and shared causal variants responding to selection across these pig populations. Negligible error rates (less than or equal to 0.02%) of false-positive associations were found when testing GPSM on gene-drop simulated genotypes, suggesting that GPSM distinguishes selection from random genetic drift in actual pig populations.ConclusionsThis work confirms the efficacy and the negligible error rates of the GPSM method in detecting selected loci in commercial pig populations. Our results suggest shared selection objectives and genetic architectures across swine populations. The identified polygenic selection highlights loci that are important to swine production.

Analysis of the Facial Measurements and Dental Arch Dimensions for the Construction of Dental Prostheses among Adult Yemenis.

To investigate the dental arch dimension (width, length, and height) and facial measurements including inner-canthal width (ICW), bizygomatic width (BZW), inter-alar width (IAW), and mouth width (MW), and to assess the correlation between these facial measurements and dental arch width (canine width [CW], inter-first premolar width [I1PW], and inter-first molar width [I1MW]), to establish a preliminary reference for artificial teeth selection in Yemeni adult. The study included 80 individuals (40 males and 40 females) with symmetrical faces and normal class I occlusion ranging in age from 20 to 35. Maxillary and mandibular stone casts were made for each individual. The dimensions of dental casts and facial measurements, including ICW, BZW, IAW, and MW, were assessed using a digital caliper. The collected data were analyzed by using the SPSS software program. The descriptive statistics for each measurement were made. Differences between males and females were tested using an independent-sample t-test with p-values below 0.05 considered significant. Pearson correlation coefficient between facial measurements and dental arch width was also done. Most dental arch dimensions and facial measurements exhibited larger mean values in the male than in the female group, with the greatest significant difference in the maxillary dental arch width and the lowest in mandibular dental arch length. A highly significant correlation is observed between ICW and maxillary canine width (CW) (r = 0.318, p = 0.004). In contrast, no significant correlation between dental arch width and BZW, IAW, and MW is shown. Within this study's limitations, the ICW can determine the ideal dimension of the artificial teeth in the anterior maxillary arch. While the other facial parameters, including BZW, IAW, and MW, cannot be used for artificial teeth selection in Yemeni populations. The findings of this study established a reference database of facial measurements and their correlation to dental arch and teeth width in Yemeni populations. So, it can be implemented in artificial teeth and dental prostheses design and construction.

An Analysis of Conservation of Biodiversity Under Indian Constitution and Judicial Response

Biodiversity is part of our daily lives and livelihood and constitutes the resources upon which families, communities, nations and future generations depend. Biodiversity can be set in a time frame so that species extinctions, the disappearance of ecological associations, or the loss of genetic variants in an extant species can be classed as loss of biodiversity. Similarly, additions to biodiversity include addition of new elements of life by mutation, by artificial breeding, by biotechnology or by ecological manipulation. A large number of factors and forces are responsible for the steep decline in the earth’s biodiversity during the last century. Most of these are caused due to tremendous increase in human population and this in turn resulted in the over exploitation of certain plant and animal resources for food, medicine, skin, fur, tusks, musk, etc., habitat loss and fragmentation, land use change and pollution. Concerns have been raised about the loss of biodiversity especially after the United Nations Conference on Environment and Development (UNCED) held at Rio de Janeiro in 1992, where loss of biodiversity was recognized as one of the most important problem of this century. This article focuses on provisions of Indian constitution for conservation of biodiversity and also judicial response for the conservation of biodiversity.

Iso-seq and RNA-seq profiling of Fenneropenaeus penicillatus: Unravelling the signaling pathway and genes involved in the ovarian development

The impediment of inadequate shrimp gonad development has adversely affected their production in the aquaculture sector. One promising strategy to enhance the quality and timing of offspring for commercial purposes is the regulation of their reproductive activity. Nevertheless, the availability of information pertaining to ovarian development in Fenneropenaeus penicillatus remains limited. To address this knowledge gap, our study employed a multi-faceted approach, integrating cutting-edge technologies such as Iso-seq, RNA-seq, RT-qPCR, histological and morphological observations. The Iso-seq generating 81,964,598 subreads with an average length of 1600 bp. This effort yielded 926,713 CCS reads and 557,043 FLNC reads, culminating in a robust set of 16,587 non-redundant full-length transcripts. This study utilized CPC, CPAT, PLEK, and pfam, to predict the numbers of long non-coding RNAs (lncRNAs). The outcomes were as follows: 5204, 4478, 7055, and 8175 lncRNAs, respectively. Our findings unveiled the intricate molecular underpinnings of ovarian development, encompassing pivotal pathways such as oocyte meiosis, insulin signaling pathway, oxytocin signaling pathway, progesterone-mediated oocyte maturation, estrogen signaling pathway, and GnRH signaling pathway. Notably, we identified specific genes—including Vtg, VgR, Sxl4, UCH, Hsp70, PP1, CDK2, Rheb, MKK3, and CDC42—that exhibited dynamic expression patterns during ovarian development. This study has produced a comprehensive dataset of full-length transcripts that holds significant potential as a genomic reference for future research on F. penicillatus. Furthermore, these insights may substantially contribute to the advancement of artificial breeding techniques and the ongoing development of sustainable aquaculture practices for F. penicillatus.

Genetic and Haplotype Diversity of Manila Clam Ruditapes philippinarum in Different Regions of China Based on Three Molecular Markers.

China has the largest production yield of Manila clam Ruditapes philippinarum in the world. Most of the clam seeds for aquaculture are mainly derived from artificial breeding in southern China, likely resulting in the loss of genetic variation and inbreeding depression. To understand the genetic and haplotype diversity of R. philippinarum, 14 clam populations sampled from different regions of China were analyzed by three molecular markers, including COI, 16SrRNA and ITS. Based on the results of the COI and ITS genes, the 14 populations showed a moderate to high level of genetic diversity, with an average haplotype diversity of 0.9242 and nucleotide diversity of 0.05248. AMOVA showed that there was significant genetic differentiation among all populations (mean FST of the total population was 0.4534). Pairwise FST analysis showed that genetic differentiation reached significant levels between Laizhou and other populations. Two Laizhou populations showed great divergence from other populations, forming an independent branch in the phylogenetic tree. The shared haplotypes Hap_2 and Hap_4 of COI appeared most frequently in most clam populations. In contrast, 16SrRNA analysis of the clam populations revealed the dominated haplotype Hap_2, accounting for 70% of the total number of individuals. The haplotype diversity of the Laizhou population (Laizhou shell-wide (KK) and Laizhou dock (LZMT)) was relatively higher than other populations, showing multiple unique haplotypes (e.g., Hap_40, Hap_41 and Hap_42). These findings of genetic and haplotype diversity of clam populations provide guiding information for genetic resource conservation and genetic improvement of the commercially important R. philippinarum.

Analyzing the pregnancy status of giant pandas with hierarchical behavioral information

As giant pandas (Ailuropoda melanoleuca) are difficult to conceive and prone to abortion, humans have turned to artificial captive breeding to increase their population. Therefore, it is crucial for their reproduction to analyze their pregnancy status accurately and promptly in artificial captive breeding. To determine whether a giant panda is pregnant, with the current methods, experts must keep a close eye on them and frequently collect their urine or blood, which requires significant resources with a high misdiagnosis rate, and will adversely affect giant pandas’ daily lives. Consequently, it is essential to rapidly advance the development of automated, precise methods that will not disrupt the pandas’ lives to analyze giant pandas’ behaviors and determine whether or not they are pregnant. In this paper, we propose an end-to-end intelligent system for predicting the pregnancy status of giant pandas and their Expected Date of Delivery (EDD). We first introduce expert knowledge to machine learning methods to solve this problem, which can significantly improve the accuracy of prediction. Experimental results show that this system achieves an accuracy of 91.5% for the pregnancy diagnosis and 0.579 days of mean average error for EDD prediction when the observation period is 5 days. Our automated system significantly reduces the need for human intervention, thus minimizing disruptions to the pandas’ daily lives. It has the potential to contribute to the health and genetic diversity of the giant pandas, as well as aid in the panda’s artificial reproduction and population growth.

Genome-wide association study (GWAS) analysis of black color trait in the leopard coral grouper (Plectropomus leopardus) using whole genome resequencing

The leopard coral grouper (Plectropomus leopardus) is a coral reef fish species that exhibits rapid and diverse color variation. However, the presence of melanoma and the high proportion of individuals displaying black color in artificial breeding have led to reduced economic and ornamental value. To pinpoint single nucleotide polymorphisms (SNPs) and potential genes linked to the black pigmentation characteristic in this particular species, This study gathered a cohort of 360 specimens from diverse origins and conducted a comprehensive genome-wide association analysis (GWAS) employing whole-genome resequencing. As a result, 57 SNPs related to the black skin trait were identified, and a grand total of 158 genes were annotated within 50 kb of these SNPs. Subsequently, GWAS was applied to three populations (LED, QHH, and QHL), and the corresponding results were compared with the analysis results of the total population. The results of the four GWAS models showed significant enrichment in Rap1 signaling pathway, melanin biosynthesis, metabolic pathways, tyrosine metabolism, cAMP signaling pathway, AMPK signaling pathway, PI3K-Akt signaling pathway, EGFR tyrosine kinase inhibitor resistance, HIF-1 signaling pathway, Ras signaling pathway, MAPK signaling pathway, etc. (p < 0.05), which were mainly associated with eleven genes (POL4, MET, E2F2, COMT, ZBED1, TYRP2, FOXP2, THIKA, LORF2, MYH16 and SOX2). Significant differences (p < 0.05) were observed in the expression of all 11 genes in the dorsal skin tissue, in 10 genes except COMT in the ventral skin tissue, and in all 11 genes in the caudal fin tissue. These findings imply that the control of body color in the P. leopardus is the result of the joint action of multiple genes and signaling pathways. These findings will contribute to a more profound comprehension of the genetic attributes that underlie the development of black skin in the vibrant P. leopardus, thus furnishing a theoretical foundation for genetic enhancement.

Full-length transcriptome analysis provides new insights into the diversity of immune-related genes in the threatened freshwater shellfish Solenaia oleivora.

Solenaia oleivora, a valuable and rare bivalve endemic to China, is becoming a threatened freshwater sepcies. However, the lack of research on its genome and immune system will hinder advances in its conservation and artificial breeding. In this study, we obtained the full-length transcriptome of S. oleivora using PacBio sequencing. A total of 21,415 transcripts with an average length of 1,726 bp were generated. Among these transcripts, 12,084 had coding sequences (CDS), of which 8,639 were annotated in 6 databases. The structure analysis identified 625 transcript factors (TFs), 8,005 long non-coding RNAs (lncRNAs), and 5,288 simple sequences repeat (SSRs). Meanwhile, massive immune genes were identified from the transcriptome of S. oleivora. In terms of non-self-identification, 97 transcripts of pattern recognition receptors (PRRs) were discovered, including peptidoglycan recognition proteins (PGRPs), gram-negative bacteria binding proteins (GNBPs), toll-like receptors (TLRs), scavenger receptors (SRs), galectins (GALs), C-type lectins (CLTs), and fibrinogen-related protein (FREPs). For pathogen elimination, 7 transcripts related to antimicrobial peptides, lysozymes, and lysosomal enzymes were identified. Moreover, 33 complement-associated transcripts were found. This study enriched the genome resources of S. oleivora and provided new insights for the study of the immune system of S. oleivora.

Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Gossypium hirsutum L.) via GWAS.

Seed vigor (SV) is a crucial trait determining the quality of crop seeds. Currently, over 80% of China's cotton-planting area is in Xinjiang Province, where a fully mechanized planting model is adopted, accounting for more than 90% of the total fiber production. Therefore, identifying SV-related loci and genes is crucial for improving cotton yield in Xinjiang. In this study, three seed vigor-related traits, including germination potential, germination rate, and germination index, were investigated across three environments in a panel of 355 diverse accessions based on 2,261,854 high-quality single-nucleotide polymorphisms (SNPs). A total of 26 significant SNPs were detected and divided into six quantitative trait locus regions, including 121 predicted candidate genes. By combining gene expression, gene annotation, and haplotype analysis, two novel candidate genes (Ghir_A09G002730 and Ghir_D03G009280) within qGR-A09-1 and qGI/GP/GR-D03-3 were associated with vigor-related traits, and Ghir_A09G002730 was found to be involved in artificial selection during cotton breeding by population genetic analysis. Thus, understanding the genetic mechanisms underlying seed vigor-related traits in cotton could help increase the efficiency of direct seeding by molecular marker-assisted selection breeding.

Robust Audio Copy-Move Forgery Detection Using Constant Q Spectral Sketches and GA-SVM

Audio recordings used as evidence have become increasingly important to litigation. Before their admissibility as evidence, an audio forensic expert is often required to help determine whether the submitted audio recordings are altered or authentic. Within this field, the copy-move forgery detection (CMFD), which focuses on finding possible forgeries that are derived from the same audio recording, has been an urgent problem in blind audio forensics. However, most of the existing methods require idealistic pre-segmentation and artificial threshold selection to calculate the similarity between segments, which may result in serious misleading and misjudgment especially on high frequency words. In this work, we present a robust method for detecting and locating an audio copy-move forgery on the basis of constant Q spectral sketches (CQSS) and the integration of a customised genetic algorithm (GA) and support vector machine (SVM). Specifically, the CQSS features are first extracted by averaging the logarithm of the squared-magnitude constant Q transform. Then, the CQSS feature set is automatically optimised by a customised GA combined with SVM to obtain the best feature subset and classification model at the same time. Finally, the integrated method, named CQSS-GA-SVM, is evaluated against the state-of-the-art approaches to blind detection of copy-move forgeries on real-world copy-move datasets with read English and Chinese corpus, respectively. The experimental results demonstrate that the proposed CQSS-GA-SVM exhibits significantly high robustness against post-processing based anti-forensics attacks and adaptability to the changes of the duplicated segment duration, the training set size, the recording length, and the forgery type, which may be beneficial to improving the work efficiency of audio forensic experts.

Interpretable artificial intelligence-assisted embryo selection improved single-blastocyst transfer outcomes: a prospective cohort study

Research questionWhat is the pregnancy and neonatal outcomes of an interpretable artificial intelligence (AI) model for embryo selection in a prospective clinical trial? DesignThis single-centre prospective cohort study was carried out from October 2021 to March 2022. A total of 330 eligible patients were assigned to their preferred groups, with 250 patients undergoing a fresh single-blastocyst transfer cycle after the exclusion criteria had been applied. For the AI-assisted group (AAG), embryologists selected the embryos for transfer based on the ranking recommendations provided by an interpretable AI system, while with the manual group, embryologists used the Gardner grading system to make their decisions. ResultsThe implantation rate was significantly higher in the AAG than the manual group (80.87% versus 68.15%, P = 0.022). No significant difference was found in terms of monozygotic twin rate, miscarriage rate, live birth rate and ectopic pregnancy rate between the groups. Furthermore, there was no significant difference in terms of neonatal outcomes, including gestational weeks, premature birth rate, birth height, birthweight, sex ratio at birth and newborn malformation rate. The consensus rate between the AI and retrospective analysis by the embryologists was significantly higher for good-quality embryos (i.e. grade 4BB or higher) versus poor-quality embryos (i.e. less than 4BB) (84.71% versus 25%, P < 0.001). ConclusionsThese prospective trial results suggest that the proposed AI system could effectively help embryologists to improve the implantation rate with single-blastocyst transfer compared with traditional manual evaluation methods.

42 (P3-7). Managing the PRRS positive sow herd with virus negative piglets – Breeding stock introduction and biosecurity

42 (P3-7). Managing the PRRS positive sow herd with virus negative piglets – Breeding stock introduction and biosecurity