Background Selection Research Articles

Comparative selective pressure analysis on mitochondrial protein-coding genes in flying squirrels (Pteromyini) and tree squirrels (Sciurini)

Different animal groups with varying locomotion modes may have unique energy requirements. Mitochondria produce adenosine triphosphate (ATP) and reactive oxygen species via oxidative phosphorylation to support organisms energy requirements. The tribes Pteromyini (flying squirrels) and Sciurini (tree squirrels), two closely related taxa within the family Sciuridae, exhibit distinct locomotion modes, energy requirements, and likely face different selective pressures on mitochondrial protein-coding genes (PCGs). We analysed 13 mitochondrial genome sequences from species belonging to the tribe Pteromyini and 117 from species belonging to the tribe Sciurini. Phylogenetic analysis revealed Pteromyini and Sciurini formed a sister relationship within the family Sciuridae. Among the 13 PCGs, ATP8 exhibited the highest dN/dS values, while COX1 showed the lowest. The background selection ratio (ω2) values for six genes (ND1, ND2, ND4, ATP6, ND5, and COX3) in Pteromyini were lower than the foreground selection ratio (ω0) values observed in Sciurini. A RELAX analysis revealed that CYTB, ND4, ATP6, and COX3 genes experienced intensified in selection strength. BUSTED analysis identified stronger signatures of diversifying selection in CYTB and ATP6, highlighting amino acid changes. MEME identified episodic diversifying selection at specific sites among eight PCGs. These findings revealed distinct selective pressures on PCGs in flying and tree squirrels.

Genealogical asymmetry under the IM model and a two-taxon test for gene flow.

Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the ABBA-BABA test being a well known example. Currently, asymmetry-based methods cannot be applied to a pair of populations and such analyses are instead performed using model-based methods. Here we investigate genealogical asymmetry under a two-population Isolation with Migration model. We focus on genealogies where the first coalescence event is between lineages sampled from different populations, as the external branches of these genealogies have equal expected length as long as there is no post-divergence gene flow. We show that unidirectional gene flow breaks this symmetry and results in the recipient population having longer external branches. We derive expectations for the probability of this genealogical asymmetry and propose a simple statistic (Am) to detect it from genome sequence data. Am provides a two-taxon test for gene flow that only requires a single unphased diploid genome from each population, with no outgroup information. We use analytic expectations and simulations to explore how recombination, unequal effective population sizes, bidirectional gene flow and background selection influence Am and find that the statistic provides unambiguous evidence for gene flow under a continent-island history. We estimate Am for genome sequence data from Heliconius butterflies and Odocoileus deer, generating results consistent with previous model-based analyses. Our work highlights a signal of gene flow overlooked to date and provides a method that complements existing approaches for investigating the demographic history of recently diverged populations.

Local adaptation can cause both peaks and troughs in nucleotide diversity within populations.

The amount of standing variation present within populations is a fundamental quantity of interest in population genetics, commonly represented by calculating the average number of differences between pairs of nucleotide sequences (nucleotide diversity, π). It is well understood that both background and positive selection can cause reductions in nucleotide diversity, but less clear how local adaptation affects it. Depending on the assumptions and parameters, some theoretical studies have emphasized how local adaptation can reduce nucleotide diversity, while others have shown that it can increase it. Here, we explore how local adaptation shapes genome-wide patterns in within-population nucleotide diversity, extending previous work to study the effects of polygenic adaptation, genotypic redundancy, and population structure. We show that local adaptation produces two very different patterns depending on the relative strengths of migration and selection, either markedly decreasing or increasing within-population diversity at linked sites at equilibrium. At low migration, regions of depleted diversity can extend large distances from the causal locus, with substantially more diversity eroded than expected with background selection. With higher migration, peaks occur over much smaller genomic distances but with much larger magnitude changes in diversity. Across spatially extended environmental gradients, both patterns can be found within a single species, with increases in diversity at the center of the range and decreases towards the periphery. Our results demonstrate that there is no universal diagnostic signature of local adaptation based on within-population nucleotide diversity, so it will not be broadly useful for explaining increased FST. However, given that neither background nor positive selection inflate diversity, when peaks are found they suggest local adaptation may be acting on a causal allele in the region.

The use of individual and collective selection, optimisation and compensation (SOC) strategies and their association with work ability among senior workers

Background Selection, optimisation, and compensation (SOC) can be important strategies for maintaining work ability as we age. This study aimed to explore differences in self-reported individual and collective use of SOC strategies across job functions, as well as their association with self-rated work ability. Methods: In the third wave of the SeniorWorkingLife study, 10,798 workers aged 50 + , across the job function categories “Office work”, “work with people”, and “work in the field of production”, replied to questions about collective and individual SOC strategies and work ability. Using multiple regression, we modelled associations between SOC and work ability. Results: Associations between SOC and work ability were generally weaker among participants working in the field of production. Both individual and collective use of selection had much weaker associations with work ability in the job functions “office work” and “working with people”. In the job function “working in the field of production”, only collective compensation was positively associated with work ability while individual selection was significantly but negatively associated with work ability. Conclusions: The use of SOC may be particularly beneficial for older employees working with people. Optimisation and compensation may be the most important SOC strategies for maintaining the work ability of older employees working with people and doing office work. For older employees working in the field of production, collective optimisation may support the maintenance of work ability while reduced work ability may be associated with the use of individual selection as a “coping strategy”.

Evolution of the correlated genomic variation landscape across a divergence continuum in the genus Castanopsis.

The heterogeneous landscape of genomic variation has been well documented in population genomic studies. However, disentangling the intricate interplay of evolutionary forces influencing the genetic variation landscape over time remains challenging. In this study, we assembled a chromosome-level genome for Castanopsis eyrei and sequenced the whole genomes of 276 individuals from 12 Castanopsis species, spanning a broad divergence continuum. We found highly correlated genomic variation landscapes across these species. Furthermore, variations in genetic diversity and differentiation along the genome were strongly associated with recombination rates and gene density. These results suggest that long-term linked selection and conserved genomic features have contributed to the formation of a common genomic variation landscape. By examining how correlations between population summary statistics change throughout the species divergence continuum, we determined that background selection alone does not fully explain the observed patterns of genomic variation; the effects of recurrent selective sweeps must be considered. We further revealed that extensive gene flow has significantly influenced patterns of genomic variation in Castanopsis species. The estimated admixture proportion correlated positively with recombination rate and negatively with gene density, supporting a scenario of selection against gene flow. Additionally, putative introgression regions exhibited strong signals of positive selection, an enrichment of functional genes, and reduced genetic burdens, indicating that adaptive introgression has played a role in shaping the genomes of hybridizing species. This study provides insights into how different evolutionary forces have interacted in driving the evolution of the genomic variation landscape.

Differential survival and background selection in cryptic trunk-dwelling arthropods in fire-prone environments

Differential survival and background selection in cryptic trunk-dwelling arthropods in fire-prone environments

Background selection for camouflage shifts in accordance with color change in an intertidal prawn.

To maximize camouflage across visually heterogeneous habitats, animals have evolved a variety of strategies, including polyphenism, color change, and behavioral background matching. Despite the expected importance of behavioral processes for mediating camouflage, such as selection for matching substrates, behavior has received less attention than color traits themselves, and interactions between color change and behavior are largely unexplored. Here, we investigated behavioral background matching in green and red chameleon prawns (Hippolyte varians) over the course of a color change experiment. Prawns were housed on mismatching green and red seaweeds for 30 days and periodically given a choice test between the same seaweeds in y-choice trials over the experiment. We found that, as prawns change color and improve camouflage (to the perspective of a fish predator), there is a reinforcing shift in behavior. That is, as prawns shift from red to green color, or vice versa, their seaweed color preference follows this. We provide key empirical evidence that plasticity of appearance (color) is accompanied by a plastic shift in behavior (color preference) that reinforces camouflage in a color changing species on its natural substrate. Overall, our research highlights how short-term plasticity of behavior and longer-term color change act in tandem to maintain crypsis over time.

Enhancing kernel oil and tailoring fatty acid composition by genomics-assisted selection for dgat1-2 and fatb genes in multi-nutrient-rich maize: new avenue for food, feed and bioenergy.

Enhancing maize kernel oil is vital for improving the bioavailability of fat-soluble vitamins. Here, we combined favourable alleles of dgat1-2 and fatb into parental lines of four multi-nutrient-rich maize hybrids (APTQH1, APTQH4, APTQH5 and APTQH7) using marker-assisted selection (MAS). Parental lines possessed favourable alleles of crtRB1, lcyE, vte4 and opaque2 genes. Gene-specific markers enabled successful foreground selection in BC1F1, BC2F1 and BC2F2, while background selection using genome-wide microsatellite markers (127-132) achieved 93% recurrent parent genome recovery. Resulting inbreds exhibited significantly higher oil (6.93%) and oleic acid (OA, 40.49%) and lower palmitic acid (PA, 14.23%) compared to original inbreds with elevated provitamin A (11.77 ppm), vitamin E (16.01 ppm), lysine (0.331%) and tryptophan (0.085%). Oil content significantly increased from 4.80% in original hybrids to 6.73% in reconstituted hybrids, making them high-oil maize hybrids. These hybrids displayed 35.70% increment in oil content and 51.56% increase in OA with 36.32% reduction in PA compared to original hybrids, while maintaining higher provitamin A (two-fold), vitamin E (nine-fold), lysine (two-fold) and tryptophan (two-fold) compared to normal hybrids. Lipid health indices showed improved atherogenicity, thrombogenicity, cholesterolaemic, oxidability, peroxidizability and nutritive values in MAS-derived genotypes over original versions. Besides, the MAS-derived inbreds and hybrids exhibited comparable grain yield and phenotypic characteristics to the original versions. The maize hybrids developed in the study possessed high-yielding ability with high kernel oil and OA, low PA, better fatty acid health and nutritional properties, higher multi-vitamins and balanced amino acids, which hold immense significance to address malnutrition and rising demand for oil sustainably in a fast-track manner.

Real-time salient object detection based on accuracy background and salient path source selection

Real-time salient object detection based on accuracy background and salient path source selection

Development of a 45K pepper GBTS liquid-phase gene chip and its application in genome-wide association studies.

Pepper (Capsicum spp.) is a vegetable that is cultivated globally and has undergone extensive domestication, leading to a significant diversification in its agronomic traits. With the advancement of genomics in pepper and the reduction in sequencing costs, the high-throughput detection of single nucleotide polymorphisms (SNPs) and small insertions-deletions (indels) has become increasingly critical for analyzing pepper germplasms and improving breeding programs. As a result, there is a pressing need for a cost-effective, high-throughput, and versatile technique suitable for both foreground and background selection in pepper breeding. In the present study, Python-based web scraping scripts were utilized to systematically extract data from published literatures and relevant sequence databases focusing on pepper genomes. Subsequent to data extraction, SNPs and indels were meticulously identified and filtered. This process culminated in the delineation of core polymorphic sites, which were instrumental in the development of specific probes. Following this, comprehensive phenotypic and genotypic analyses were conducted on a diverse collection of 420 pepper germplasms. Concurrently, a genome-wide association study (GWAS) was conducted to elucidate the genetic determinants of helical fruit shape in peppers. In this study, a 45K pepper Genotyping-By-Target-Sequencing (GBTS) liquid-phase gene chip was developed on the GenoBaits platform. This chip is composed of 45,389 probes, of which 42,535 are derived from core polymorphic sites (CPS) in the background genetic landscape, while 2,854 are associated with foreground agronomic traits, spanning across 43 traits. The CPS probes are spaced at an average interval of 68 Kb. We have assessed the performance of this chip on 420 pepper germplasms, with successful capture of target DNA fragments by 45,387 probes. Furthermore, the probe capture ratio surpassed 70% in 410 of the 420 germplasms tested. Using this chip, we have efficiently genotyped 273 germplasms for spiciness levels and elucidated the genetic relationships among 410 pepper germplasms. Our results allowed for precise clustering of sister lines and C. chinense germplasms. In addition, through a GWAS for helical fruit shape, we identified three quantitative trait loci (QTLs): heli2.1, heli11.1, and heli11.2. Within the heli11.1 QTL, a gene encoding the tubulin alpha chain was identified, suggesting its potential role in the helical growth pattern of pepper fruits. In summary, the 45K pepper GBTS liquid-phase gene chip offers robust detection of polymorphic sites and is a promising tool for advancing research into pepper germplasm and the breeding of new pepper varieties.

IMPROVEMENT OF HIGH AMYLOSE CONTENT IN CH1 RICE VARIETY BY MARKER ASSISTED PSEUDO-BACKCROSS BREEDING

The objective of this research was to introgression of high amylose content into CH1 rice variety by using pseudo-backcrossing breeding. Crossing between CH1 and RD49 was performed to produce F1 progenies. After that, the progenies will backcross to CH1 to develop BC1F1 population. Then, the selected plants from the BC1F1 population were continuously selfed to develop BC1F2 and BC1F3 populations, respectively. For marker assisted selection, the OSR19 DNA marker that is specific to Wx gene was used for assisting the selection of plants with high amylose content in foreground selection to choose favorite genotype. Total 67 SSR markers used genetic background selection was done twice in BC1F1 and BC1F2 populations. The results showed that selection could be achieved for BC1F1 and BC1F2 plants having high amylose content and first highest ranking of genetic background similar to recurrent parent exhibited 91.04 and 97.76 percent, respectively. The marker assisted selection could accelerate 4 generations in backcross breeding program. The BC1F3 seeds of 6 selected lines were planted in paddy field for preliminary yield test. It was found that agronomic characters and yield of the selected lines were not statistically different from those of CH1 variety and high amylose content as donor parent.

대학 입학전형 선택의 영향 요인 분석

Objectives The purpose of this study is to analyze the factors that affect the choice of admission types among college students, including personal background, self-efficacy, autonomy, learning motivation, and major selection motivation. Methods To achieve this goal, a survey was conducted on 1,099 students enrolled at A University in Seoul. Factors influencing admission type preferences were analyzed using chi-square tests, one-way ANOVA, and multinomial logistic regression. Results Differences in admission type preferences emerged based on students' backgrounds, including the region and type of their high school, and the highest educational attainment of their guardians. Among personal characteristics, significant disparities in admission-type preferences were observed based on self-efficacy and major selection motivation. In relation to the origin of the high school, as the region shifted to Seoul and the metropolitan area, and as the educational attainment of male guardians increased, along with stronger intrinsic motives for major selection, the likelihood of opting for the regular comprehensive evaluation process increased. Conversely, in cases where the originating high school was located in urban or smaller cities, and when female guardians possessed higher educational qualifications, along with stronger extrinsic motives for major selection, there was an elevated probability of preferring the regular admission method. Conclusions Given the variations in the backgrounds and attributes of students selecting university admission types, universities should take a keen interest not only in the selection process but also in academic and career support.

Biases in ARG-Based Inference of Historical Population Size in Populations Experiencing Selection.

Inferring the demographic history of populations provides fundamental insights into species dynamics and is essential for developing a null model to accurately study selective processes. However, background selection and selective sweeps can produce genomic signatures at linked sites that mimic or mask signals associated with historical population size change. While the theoretical biases introduced by the linked effects of selection have been well established, it is unclear whether ancestral recombination graph (ARG)-based approaches to demographic inference in typical empirical analyses are susceptible to misinference due to these effects. To address this, we developed highly realistic forward simulations of human and Drosophila melanogaster populations, including empirically estimated variability of gene density, mutation rates, recombination rates, purifying, and positive selection, across different historical demographic scenarios, to broadly assess the impact of selection on demographic inference using a genealogy-based approach. Our results indicate that the linked effects of selection minimally impact demographic inference for human populations, although it could cause misinference in populations with similar genome architecture and population parameters experiencing more frequent recurrent sweeps. We found that accurate demographic inference of D. melanogaster populations by ARG-based methods is compromised by the presence of pervasive background selection alone, leading to spurious inferences of recent population expansion, which may be further worsened by recurrent sweeps, depending on the proportion and strength of beneficial mutations. Caution and additional testing with species-specific simulations are needed when inferring population history with non-human populations using ARG-based approaches to avoid misinference due to the linked effects of selection.

Marker-assisted introgression lines of elite Indian mustard (Brassica juncea) cultivars for resistance against white rust (Albugo candida)

White rust caused by Albugo candida is a major biotic constraint responsible for significant yield loss in mustard production across all mustard-growing regions. This experiment was conducted with the aim of developing WRR lines of Indian mustard using the MABB approach. The elite mustard cultivars of Brassica juncea viz., DRMR150-35, DRMRIJ-31 and NRCDR-02 were used as the recurrent parent, whereas BioYSR, BEC-144 and Donskaja were taken as donors. A parental polymorphism survey using 315 microsatellites (SSR) was done among recurrent and donor parents. To confirm introgression of white rust resistance gene foreground selection was performed using Arabidopsis-derived IP markers that are linked to the white rust loci AcB1-A5.1 (At2g36360) for Donskaja and BioYSR and AcB1-A4.1 (At5g41560) for BEC-144coupled with background selection and phenotypic selection for highest recurrent parent genome recovery. Finally, 19 BC3F3 lines were obtained, which led to the identification of 5 highly white rust-resistant lines with RPG recovery percentage of ˃90%. These selected improved lines showed a resistance response with mean %WR severity (100 DAS) below 5% and possess the agro-morphological characters at par to their respective recurrent parent. These lines have good potential for future release and demonstrated MABB as a valuable tool for expediency, enrichment and precision in accelerating the development of new disease-resistant Indian mustard varieties.

Selection leads to false inferences of introgression using popular methods.

Detecting introgression between closely related populations or species is a fundamental objective in evolutionary biology. Existing methods for detecting migration and inferring migration rates from population genetic data often assume a neutral model of evolution. Growing evidence of the pervasive impact of selection on large portions of the genome across diverse taxa suggests that this assumption is unrealistic in most empirical systems. Further, ignoring selection has previously been shown to negatively impact demographic inferences (e.g. of population size histories). However, the impacts of biologically realistic selection on inferences of migration remain poorly explored. Here, we simulate data under models of background selection, selective sweeps, balancing selection, and adaptive introgression. We show that ignoring selection sometimes leads to false inferences of migration in popularly used methods that rely on the site frequency spectrum. Specifically, balancing selection and some models of background selection result in the rejection of isolation-only models in favor of isolation-with-migration models and lead to elevated estimates of migration rates. BPP, a method that analyzes sequence data directly, showed false positives for all conditions at recent divergence times, but balancing selection also led to false positives at medium-divergence times. Our results suggest that such methods may be unreliable in some empirical systems, such that new methods that are robust to selection need to be developed.

Pyramiding aphid resistance genes into the elite cowpea variety, Zaayura, using marker-assisted backcrossing

The cowpea aphid (Aphis cracivora) is a cosmopolitan insect pest that causes economic damage on cowpea. Although the pest persists at all the growth stages of the crop, in West Africa, aphids are the only major insect pests that farmers regularly control at the vegetative stage. Thus, deploying aphid-resistant crop varieties can reduce farmers' expenditure on insecticide. The availability of different biotypes of the pest and reports of resistance breakdown necessitates pyramiding of sources of aphid resistance to develop a more robust genotype for durable resistance. Two aphid-resistance genes, sourced from SARC-1-57-2 and IT97K-556-6, were introgressed through gene pyramiding technique into a farmers’ preferred cowpea variety, Zaayura, using marker-assisted backcrossing. A simple sequence repeat (SSR) marker, CP 171F/172R, and an allele-specific single nucleotide polymorphism (SNP) marker, 1_0912, were used for foreground selection of the SARC-1-57-2 and IT97K-556-6 aphid resistance genes, respectively. A stepwise backcross approach was used to introgress the major aphid resistance QTL (QAc-vu7.1) from IT97K-556-6 into Zaayura using the marker 1_0912 coupled with intermittent screening under artificial aphid infestation. After the fourth backcross generation, three heterozygous BC4F1 of Zaayura/TT97K-556-6 were intercrossed to Zaayura Pali to develop intercross F1 (ICF1). Three true ICF1 hybrids allowed to self to produce ICF2. Five (5) out of 48 ICF2 plants which were genotyped with the two foreground markers had the two aphid resistance genes fixed in the double homozygous dominant state. For background selection, out of 192 allele-specific markers screened, only 47 polymorphic markers were identified and used for the background analysis of the pyramided lines. The recurrent parent genome recovery ranged from 72 to 93.8 %. ICF2_Zaa/556/SARC-P6 had the highest recurrent parent genome and the least heterozygosity among the five improved lines. The five pyramided lines showed superior resistance under artificial aphid infestation as compared to the two donor parents with damage scores ranging from 2.0 to 2.3. On the field, however, there were no significant differences between the pyramided lines and their recurrent parent for all the agronomic traits measured except for grain yield. The pyramided lines do not only stand the chance of being released as new varieties but are also valuable genetic resources for other breeding programs that seek to improve cowpea for aphid resistance.

High Prevalence and Clinical Relevance of Intrapulmonary Vascular Dilatations in Patients Undergoing TIPS Implantation

Background and AimsConsiderate patient selection is vital to ensure best possible outcomes after transjugular intrahepatic portosystemic shunt (TIPS) insertion. However, data regarding the impact of intrapulmonary vascular dilatations (IPVD) or hepatopulmonary syndrome (HPS) on the clinical course after TIPS implantation is lacking. Hence, this study aimed to investigate the relevance of IPVD and HPS in patients undergoing TIPS implantation. MethodsContrast enhanced echocardiography and blood gas analysis were utilized to determine presence of IPVD and HPS. Multivariable competing risk analyses were performed to evaluate cardiac decompensation (CD), hepatic decompensation (HD) and liver transplant (LTx)-free survival within one-year of follow up. ResultsOverall, 265 patients were included, of whom 136 had IPVD and 71 fulfilled the HPS criteria. Patients with IPVD had lower Freiburg index of post-TIPS survival (FIPS) scores, lower creatinine and more often received a TIPS because of variceal bleeding. Presence of IPVD was associated with a significantly higher incidence of CD (HR: 1.756 95%CI: 1.011-3.048 p=0.046) and HD (HR: 1.841 95%CI: 1.255-2.701 p=0.002). However, LTx-free survival was comparable between patients with and without IPVD (HR: 1.081 95%CI: 0.630-1.855, p=0.780). Patients with HPS displayed a trend towards more CD (HR: 1.708 95%CI: 0.935-3.122, p=0.082) and HD (HR: 1.458 95%CI: 0.934-2.275, p=0.097) that failed to reach statistical significance. LTx-free survival did not differ in those with HPS compared to patients without HPS, respectively (HR: 1.052 95%CI: 0.577-1.921, p=0.870). ConclusionScreening for IPVD before TIPS implantation could help to further identify patients at higher risk of cardiac and hepatic decompensation.

Marker assisted breeding of Sub1 introgressed rice (Oryza sativa L.) lines and identification of stable variety MTU 1232 suitable for flood prone ecosystem

The Development of flood-tolerant rice varieties is a prerequisite for climate resilience in flood-prone areas. The present study aimed to develop a stable, high, yielding, and tolerant rice variety against flash floods and stagnant flooding across multiple environments. Sub1A was incorporated into a popular rice variety MTU 1075 using Swarna-sub1 as a donor to generate BC3F5 families. Sub1BC2 was used as a foreground marker for selection, a proxy for the Sub1A gene. RM23865 and RM464 on Chromosome 9 were used as recombinant markers. Backcross families from the BC3F2 generation were evaluated under two weeks of flash floods 15 days after transplanting. This was followed by stagnant flooding and survived BC3F4 families were used for background selection using a 50K high-density SNP chip. The nine best families identified were included in the field trial evaluation under eight environments. Consequently, MTU Rice 1232 was identified as a high-yielding, flood-tolerant rice variety using Additive Main effects and Multiplicative Interaction stability analysis. The MTU Rice 1232 ranked first by the Best linear unbiased prediction (BLUP) based ranking parameters and 4th based on stability parameters ranking. This flood-tolerant rice variety can tolerate both flash floods and stagnant flooding and possesses an 80% survival rate. It has a yield potential of 3792 Kg ha-1 under severe floods and 6000 Kg ha-1 under normal conditions.

Protein quality enhancement in temperate corn through introgression of o2o2 using marker assisted backcross and shuttle breeding

Abstract Quality protein maize (QPM) has protein quality of opaque 2 (>0.074% tryptopan) with endosperm modifiers which turn its kernels vitreous that is similar to normal maize. Use of QPM as a cereal can significantly improve daily intake of lysine and tryptophan for humans and livestock. However QPM cultivars have lower yields due to trait compensation. Therefore, a breeding programme was carried out to convert parental lines of Shalimar maize hybrid 5 (SMH-5) viz. IML-187 and BML-6 into QPM versions. Marker polymorphism was worked out in donors and recipients. IML-187 was crossed with DQL-2029-1 and BML-6 was crossed with DQL-779-2-9. The first and second backcross generations involving IML-187 as recurrent parent were marked as BC1F1 (A) and BC2F1 (A) respectively, whereas those involving BML-6 were designated as BC1F1 (B) and BC2F1 (B) respectively. The BC2F2 lines derived from two generation of backcrossing coupled with SSR marker and phenotypic background and foreground selection were advanced to BC2F3. Approximately 80–90% of RPG similarity was observed in BC2F2 lines. Eight lines namely IML-187 × DQL-2029-1- BC2F3:06, 07 and 23: BML-6 × DQl-779-2-9: 02,04,09,20 and 13 were identified from BC2F3 to have tryptophan higher than 0.075% and <25% opaqueness. These lines were used for trait fixing and crosses were made to produce QPM version of SMH-5. Six improved versions of SMH-5 were selected for higher grain yield and tryptophan content and are to be employed in further testing and varietal release in Northern Hill Zone (NHZ) in India.

Prediction of embryo euploidy and pregnancy outcome by blastocyst morphology and development speed for women receiving single embryo transfer

Background Selection of high-quality blastocysts is the most important factor determining the success of assisted reproductive technology. The objective of this study is to assess the values of blastocyst morphological quality and development speed for predicting euploidy and clinical pregnancy outcome. Methods A total of 155 preimplantation genetic testing cycles including 959 blastocysts and 154 euploid blastocyst transfer cycles conducted between January 2018 and December 2019 were retrospectively analysed. The associations of blastocyst morphological quality and development speed (D) with chromosomal status, clinical pregnancy rate, early miscarriage rate, and ongoing pregnancy rate were evaluated by univariate and multivariate regression. Results The euploidy rate of development speed D5 blastocysts was significantly greater than that of D6 blastocysts (61.4% vs. 38.1%, P < 0.001), and the euploid rate of morphologically high-grade blastocysts was significantly greater than that of non-high-grade blastocysts. Development speed D5 (OR = 1.6, 95% CI 1.2–2.2, P = 0.02) and high-grade morphology (OR = 2.1, 95% CI 1.5–2.9, P = 0.01) were independent predictors of euploidy. The ongoing pregnancy rate of D5 blastocysts was significantly higher than that of D6 blastocysts (62.3% vs. 43.8%, P = 0.04). Transfer of euploid blastocysts with high-grade morphology resulted in a greater ongoing pregnancy rate than transfer of non-high-grade euploid blastocysts (60.7% vs. 43.2%, P = 0.049). Alternatively, D6 development speed was an independent risk factor for early pregnancy loss after euploid blastocyst transfer. Multivariate regression analysis adjusting for confounding factors identified maternal age, blastocyst development speed, and blastocyst morphological grade as independent predictors of euploidy but not of clinical pregnancy. Conclusion The recommended sequence of embryo transfer based on the present study is D5 high-grade > D6 high-grade > D5 non-high-grade > D6 non-high-grade.