Background Selection Research Articles

Evaluation of Improved drought-tolerant parental lines of KMR3R for fertility restoration by molecular analysis

The present investigation was carried out to identify fertility restoration in improved drought tolerant parental lines with ideal agronomic trait performances and their utilization in the hybrid rice breeding program. Backcross derived lines obtained from a cross between a drought-tolerant Vandana NIL (donor, possessing qDTY12.1 and qDTY1.1) and a drought susceptible restorer, KMR3R (recurrent parent, possessing Rf3 and Rf4 genes). Based on foreground and background selection, the backcross population was advanced to BC2 F4 population by stringent Marker-Assisted Backcross Breeding (MABB). Molecular markers were utilized in the marker assisted restorer selection in WA-CMS from large source of nurseries to keep away from regular test cross nursery (TCN) in the hybrid rice breeding technology. The tightly linked/or gene-specific markers viz., RM6100, RMS-PPR-9-1, DRCG-Rf4-14, for Rf4 on chromosome 10, and DRRM Rf3-10, RM 10313, and RMS-SF21-5 for Rf3 located on chromosome 1 were used to screen for the presence or absence of specific restorer allele in the population. 71 improved drought-tolerant backcross inbred lines (BILs), including checks, and parents were screened for their fertility restoration. Results were skewed in their frequency distribution by showing 48.48% of Rf3 and Rf4 genes (Rf3Rf3/Rf4Rf4). These double allelic combination containing genotypes exhibit better fertility restoration than any of single Rf3Rf3/rf4rf4 or rf3rf3/Rf4Rf4 individually. Ultimately ten genotypes were identified as complete restorers (RP6340 NPVR1, RP6340 NPVR3, RP6340 NPVR10, RP 6340 NPVR24, RP6340 NPVR27, RP6340 NPVR32, RP6340 NPVR48, RP6340 NPVR52, RP6340 NRR5 and RP6340 NRR11) with drought QTLs for drought-prone lowland ecosystems and can be utilized in the hybrid rice breeding Programme under unfavorable drought ecologies

A New Breeding Strategy towards Introgression and Characterization of Stay-Green QTL for Drought Tolerance in Sorghum

Several marker-assisted selection (MAS) or backcrossing (MAB) approaches exist for polygenic trait improvement. However, the implementation of MAB remains a challenge in many breeding programs, especially in the public sector. In MAB introgression programs, which usually do not include phenotypic selection, undesired donor traits may unexpectedly turn up regardless of how expensive and theoretically powerful a backcross scheme may be. Therefore, combining genotyping and phenotyping during selection will improve understanding of QTL interactions with the environment, especially for minor alleles that maximize the phenotypic expression of the traits. Here, we describe the introgression of stay-green QTL (Stg1–Stg4) from B35 into two sorghum backgrounds through an MAB that combines genotypic and phenotypic (C-MAB) selection during early backcross cycles. The background selection step is excluded. Since it is necessary to decrease further the cost associated with molecular marker assays, the costs of C-MAB were estimated. Lines with stay-green trait and good performance were identified at an early backcross generation, backcross two (BC2). Developed BC2F4 lines were evaluated under irrigated and drought as well as three rainfed environments varied in drought timing and severity. Under drought conditions, the mean grain yield of the most C-MAB-introgression lines was consistently higher than that of the recurrent parents. This study is one of the real applications of the successful use of C-MAB for the development of drought-tolerant sorghum lines for drought-prone areas.

Molecular Breeding for Improving Productivity of Oryza sativa L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, qDTY12.1.

Increasing rice production is quintessential to the task of sustaining global food security, as a majority of the global population is dependent on rice as its staple dietary cereal. Among the various constraints affecting rice production, reproductive stage drought stress (RSDS) is a major challenge, due to its direct impact on grain yield. Several quantitative trait loci (QTLs) conferring RSDS tolerance have been identified in rice, and qDTY12.1 is one of the major QTLs reported. We report the successful introgression of qDTY12.1 into Pusa 44, a drought sensitive mega rice variety of the northwestern Indian plains. Marker-assisted backcross breeding (MABB) was adopted to transfer qDTY12.1 into Pusa 44 in three backcrosses followed by four generations of pedigree selection, leading to development of improved near isogenic lines (NILs). Having a recurrent parent genome (RPG) recovery ranging from 94.7–98.7%, the improved NILs performed 6.5 times better than Pusa 44 under RSDS, coupled with high yield under normal irrigated conditions. The MABB program has been modified so as to defer background selection until BC3F4 to accelerate generational advancements. Deploying phenotypic selection alone in the early backcross generations could help in the successful recovery of RPG. In addition, the grain quality could be recovered in the improved NILs, leading to superior selections. Owing to their improved adaptation to drought, the release of improved NILs for regions prone to intermittent drought can help enhance rice productivity and production.

Chromosome Fusion Affects Genetic Diversity and Evolutionary Turnover of Functional Loci but Consistently Depends on Chromosome Size.

Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with a recent chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 20 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. When fused, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.

Deriving tropical gynoecious inbred backcross lines from exotic pickling cucumber using marker assisted backcross breeding

Indian cucumber cultivars are basically monoecious and vigorous in nature with many lateral branches but they are poor in productivity. The present study was aimed to introgress gynoecious trait (F locus) from pickling cucumber line (Gy14) into elite Indian cultivar Pusa Uday using marker assisted backcross breeding. Based on allelic diversity analysis, the allele numbers per locus ranged from 2 to 3 in BC1F3 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.55. The heterozygosity expected (He) mean was 0.28 (range 0.03 to 0.50) which was higher than mean Ho (0.18) and mean polymorphic information content (PIC) for 87 markers was 0.23. Whereas the allele numbers per locus was 2 in BC2F2 and the observed heterozygosity (Ho) was ranged from 0.01 to 0.56. The mean expected heterozygosity (He) was 0.24 which was higher than mean Ho (0.17) and the mean PIC value was 0.19. The gynoecism (F locus) was introgressed in the Indian slicing cucumber cv. Pusa Uday though backcross breeding accompanied by foreground and background selections. The foreground selection was performed with one dominant SCAR marker, and 3 SSR markers (SSR 00233, SSR 15516 and SSR13251). A total of 87 polymorphic markers spanning genetic distance of 1031 cM with an average distance of 12.9 cM between adjacent markers were used for background selection. The genome recovery of the individuals in BC1F3 population was ranged from 62.64% to 93.10% while among BC2F2 plants it was ranged from 89.66% to 95.40%. Four inbred backcross lines (IBL) were selected from backcross populations (BC1F4 and BC2F3) those were purely gynoecious even at 45°C with more than 5 lateral branches. Hence, marker assisted backcross breeding served as a potential approach for precise introgression of the gynoecy (F locus) from picking cucumber to Indian slicing cucumber.

Novel selection paradigms for endovascular stroke treatment in the extended time window

Background and purposeThe optimal selection methodology for stroke thrombectomy beyond 6 hours remains to be established.MethodsReview of a prospectively collected database of thrombectomy patients with anterior circulation strokes, adequate CT...

Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.

A current debate within population genomics surrounds the relevance of patterns of genomic differentiation between closely related species for our understanding of adaptation and speciation. Mounting evidence across many taxa suggests that the same genomic regions repeatedly develop elevated differentiation in independent species pairs. These regions often coincide with high gene density and/or low recombination, leading to the hypothesis that the genomic differentiation landscape mostly reflects a history of background selection, and reveals little about adaptation or speciation. A comparative genomics approach with multiple independent species pairs at a timescale where gene flow and ILS are negligible permits investigating whether different evolutionary processes are responsible for generating lineage-specific versus shared patterns of species differentiation. We use whole-genome resequencing data of 195 individuals from four Ficedula flycatcher species comprising two independent species pairs: collared and pied flycatchers, and red-breasted and taiga flycatchers. We found that both shared and lineage-specific FST peaks could partially be explained by selective sweeps, with recurrent selection likely to underlie shared signatures of selection, whereas indirect evidence supports a role of recombination landscape evolution in driving lineage-specific signatures of selection. This work therefore provides evidence for an interplay of positive selection and recombination to genomic landscape evolution.

Development of Rice Varieties Adaptive to Nontidal Swampland using MABC: Growth Characteristics of Parent Plant and F1 Result

Lowland swamps have enormous potential and have been proven to provide significant contributions as a buffer in the national food security system. Rice farmers in non-tidal swamplands of South Sumatra plant rice at the end of the rainy season, because they wait for the water to recede, and therefore rice plants are very vulnerable to submerged stress in the vegetative phase and drought stress in the generative phase. This study aims to obtain rice varieties that are adaptive to these conditions and superior to lowland swamp agro-ecosystems. The research was conducted at the Plant Physiology Laboratory and Green House of Department of Agronomy, Faculty of Agriculture, Sriwijaya University. In this study, reciprocal crosses were carried out between Inpago 5 and Inpara 8 rice varieties. Inpago 5 variety was used because it has tolerant characters to drought stress in the generative phase and also has high production in farmers’ nontidal swampland. Inpara 8 has a Sub1 gene so that resistant to submerged stress in the vegetative phase. The results showed that both varieties had different characters in their growth and yield. Both varieties were crossed reciprocally and the success of crossing was more than 50%. F1 plants will be backcrossed with their female parents to get BC1F1 plants, and then selected using the MABC method [foreground selection, phenotypic selection, and background selection]. From the results of the MABC selection process, there will be BC1F1 plants with the genome proportion close to the female parent and confirmed to have the Sub1 gene.

Introgression of Recombinant 1RSWR.1BL Translocation and Rust Resistance Genes in Bread Wheat cv. HD2967 Through Marker-Assisted Selection

Bread wheat (Triticum aestivum L.) is one of the major cereal crops utilized worldwide for bread making. The presence of secalin locus on 1RS leads to the sticky dough and poor bread-making quality of wheat. In the present study, two donor parents, one with distal rye chromatin (1RS44:38) and another with distal wheat chromatin (Pavon MA1) without secalin, and one recipient elite wheat cultivar HD2967 were used. In 1RS44:38, the distal rye region has the Pm8 gene to which the QTL for superior root traits is linked, while in Pavon MA1 with Glu-B3/Gli-B1, the Pm8 gene was found to be absent. This distal rye region having root trait QTL was introgressed into the HD2967 derivatives using marker-assisted backcross selection. The derivatives with distal rye region introgression had higher root biomass, drought resistance, and 6–8% higher yield than the recipient parent cultivar. HD2967 is highly susceptible to yellow rust. Therefore, in the second backcross, the rust-resistant version of HD2967 (Lr57 + Yr40) was used to introgress rust resistance in the derivatives. Background selection was done using polymorphic wheat anchored SSR markers of A, B, and D genomes of wheat which led to the selection of derivatives with > 90% background of the recipient cultivar. The significant findings in this study include higher root biomass, improved yield, rust resistance in the derivatives, and retaining the alleles of Glu-B3/Gli-B1 along with Pm8 and the absence of secalin.

Marker-assisted stacking of null Kunitz trypsin inhibitor and off-flavour generating lipoxygenase-2 in soybean

AbstractSoybean varieties genetically free from Kunitz trypsin inhibitor (KTI) and lipoxygenase-2 (Lox2) are desirable to increase human consumption, as the former is an antinutritional factor that affects protein digestibility while the latter is a principal contributor to off-flavour. In the present investigation, soybean genotypes free from both these undesirable components were developed by introgression of null allele of Lox2 from NRC109 (lox2lox2) into two KTI-free soybean genotypes derived from genotypes JS97-52 and NRC7. Foreground selection of plants in F1, F2, BC1F1, BC1F2, BC2F1 and BC2F2 generations developed from two cross combinations i.e. NRC7-derived KTI-free genotype (N7KTIF)×NRC109 (parental combination 1) and JS97-52 derived KTI free genotype (JKTIF)×NRC109 (parental combination 2) was performed using null allele specific markers and tightly linked simple sequence repeat (SSR) markers for both KTI and Lox2 genes for the identification of homozygous recessive (titilox2lox2) plants. Background selection was performed using 239 and 241 polymorphic SSR markers across the genome. This resulted in the development of 9 and 13 soybean lines stacked for null alleles of both KTI and Lox2 (titilox2lox2) exhibiting recurrent parent genome content more than 97 and 96%, respectively. Days-to-flowering, days-to-maturity, 100-seed weight and yield per plant of the stacked lines developed from both the parental combinations were at par with the respective recurrent parents.

High-dose-rate brachytherapy with external beam radiotherapy versus low-dose-rate brachytherapy with or without external beam radiotherapy for clinically localized prostate cancer

To compare the outcomes of localized prostate cancer treatment with high-dose-rate brachytherapy (HDR-BT) and low-dose-rate brachytherapy (LDR-BT), we examined 924 patients treated with HDR-BT + external beam radiotherapy (EBRT) and 500 patients treated with LDR-BT ± EBRT using multi-institutional retrospective data. The HDR-BT treated advanced disease with more hormonal therapy than LDR-BT. To reduce background selection bias, we performed inverse probability of treatment weighting (IPTW) analysis using propensity scores and excluded patients with T3b-4 disease/ initial prostate-specific antigen (PSA) levels > 50 ng/ml. The actuarial 5-year biochemical control rates (5y-bNED) were 96.3% and 95.7% in the HDR-BT and LDR-BT groups, respectively. The corresponding values were 100% and 96.5% in the low-risk group; 97.4% and 97.1% in the intermediate-risk group (97.2% and 97% in the higher titer group and 97.5% and 94.6% in the lower titer group, respectively); and 95.7% and 94.9% in the selected high-risk group, respectively. IPTW correction indicated no significant difference among the groups. The 5y-bNED in the HDR-BT + EBRT, LDR-BT + EBRT, and LDR-BT alone groups were 96.3%, 95.5%, and 97%, respectively (P = 0.3011). The corresponding values were 97.4%, 94.7%, and 96.6% (P = 0.1004) in the intermediate-risk group (97.5%, 100%, and 94.5% in the lower titer group [P = 0.122] and 97.2%, 96.2%, and 100% [P = 0.664] in the higher titer group, respectively) and 95.7%, 95.5%, and 100% (P = 0.859) in the high-risk group, respectively. The HDR-BT group showed a lower incidence of acute grade ≥ 2 genitourinary toxicities; the incidence of other early and late grade ≥ 2 toxicities were similar between the HDR-BT and LDR-BT groups. Acute genitourinary toxicity predicted the occurrence of late genitourinary toxicity. EBRT increased the risk of grade ≥ 2 gastrointestinal toxicity. HDR-BT + EBRT is a good alternative to LDR-BT ± EBRT for low-, intermediate-, and selected high-risk patients.

Enhancing backcross programs through increased recombination

BackgroundIntrogression of a quantitative trait locus (QTL) by successive backcrosses is used to improve elite lines (recurrent parent) by introducing alleles from exotic material (donor parent). In the absence of selection, the proportion of the donor genome decreases by half at each generation. However, since selection is for the donor allele at the QTL, elimination of the donor genome around that QTL will be much slower than in the rest of the genome (i.e. linkage drag). Using markers to monitor the genome around the QTL and in the genetic background can accelerate the return to the recurrent parent genome. Successful introgression of a locus depends partly on the occurrence of crossovers at favorable positions. However, the number of crossovers per generation is limited and their distribution along the genome is heterogeneous. Recently, techniques have been developed to modify these two recombination parameters.ResultsIn this paper, we assess, by simulations in the context of Brassicaceae, the effect of increased recombination on the efficiency of introgression programs by studying the decrease in linkage drag and the recovery of the recurrent genome. The simulated selection schemes begin by two generations of foreground selection and continue with one or more generations of background selection. Our results show that, when the QTL is in a region that initially lacked crossovers, an increase in recombination rate can decrease linkage drag by nearly ten-fold after the foreground selection and improves the return to the recurrent parent. However, if the QTL is in a region that is already rich in crossovers, an increase in recombination rate is detrimental.ConclusionsDepending on the recombination rate in the region targeted for introgression, increasing it can be beneficial or detrimental. Thus, the simulations analysed in this paper help us understand how an increase in recombination rate can be beneficial. They also highlight the best methods that can be used to increase recombination rate, depending on the situation.

Model based patient pre-selection for intensity-modulated proton therapy (IMPT) using automated treatment planning and machine learning

Background and purposePatient selection for intensity modulated proton therapy (IMPT), using comparative photon therapy planning, is workload-intensive and time-consuming. Pre-selection aims at avoidance of manual IMPT planning for patients that are in the end ineligible. We investigated the use of machine learning together with automated IMPT treatment planning for pre-selection of head and neck cancer patients, and validated the methodology for the Dutch model based selection (MBS) approach. Materials & methodsFor forty-five head and neck patients with a previous MBS, an IMPT plan was generated with non-clinical, fully-automated planning. Dosimetric differences of these plans with the corresponding previously generated photon plans, and the outcomes of the former MBS, were used to train a Gaussian naïve Bayes classifier for MBS outcome prediction. During training, strong emphasis was placed on avoiding misclassification of IMPT eligible patients (i.e. false negatives). ResultsPre-selection with the classifier resulted in 0 false negatives, 12 (27%) true negatives, 27 (60%) true positives, and only 6 (13%) false positive predictions. Using this pre-selection, the number of formal selection procedures with involved manual IMPT planning that resulted in a negative outcome could be reduced by 67%. ConclusionWith pre-selection, using machine learning and automated treatment planning, the percentage of patients with unnecessary manual IMPT planning for MBS could be drastically reduced, thereby saving costs, labor and time. With the developed approach, larger patient populations can be screened, and likely bias in pre-selection of patients can be mitigated by assisting the physician during patient pre-selection.

Marker-assisted gene pyramiding (MAGP) for semi dwarfed bacterial blight resistance genes into traditional basmati variety “Ranbir Basmati”

Evolution of new virulent races has led to increased sensitiveness of the traditional basmati varieties to bacterial blight (BB) disease. Among the traditional basmati varieties, Ranbir Basmati is tall statured variety, and are susceptible to BB diseases. The variety has thin stem and prone to lodging leading to significant yield losses as well as deteriorate the grain qualities. In the present study, the marker-assisted backcross breeding (MABB) strategy were used for simultaneous stepwise transfer of two major BB resistance genes (Xa21 and xa13) along with a dwarfing gene (sd1) into Ranbir Basmati. The molecular markers viz., pTA 248, xa13prom and h linked to Xa21, xa13 and sd1, respectively were used in MABB programme. Both foreground and background selection approaches are used for pyramiding of genes of interest into Ranbir Basmati. The crosses were attempted for pyramiding the BB resistance genes along with dwarfing gene from Punjab Basmati 4 (Xa21, xa13 and sd1) into Ranbir Basmati. MABB programme was carried out up to BC2F5 generations. In total five semi-dwarf pyramided lines namely, SBTIL25, SBTIL39, SBTIL80, SBTIL121 and SBTIL31 have been identified for further field screening. These pyramided lines possess superior length/width ratio, excellent cooking properties and pleasant aroma. These five lines have been further evaluated for morpho-physiological and quality traits, and can be serve as potential donors for different rice pre-breeding programmes. These promising pyramided lines in bulk will be subjected to testing in multi-location and replicated trial for yield and disease resistance for their possible release as variety.

Addressing Darwin's dilemma: Can pseudo-overdominance explain persistent inbreeding depression and load?

Darwin spent years investigating the effects of self-fertilization, concluding that "nature abhors perpetual self-fertilization." Given that selection purges inbred populations of strongly deleterious mutations and drift fixes mild mutations, why does inbreeding depression (ID) persist in highly inbred taxa and why do no purely selfing taxa exist? Background selection, associations and interference among loci, and drift within small inbred populations all limit selection while often increasing fixation. These mechanisms help to explain why more inbred populations in most species consistently show more fixed load. This drift load is manifest in the considerable heterosis regularly observed in between-population crosses. Such heterosis results in subsequent high ID, suggesting a mechanism by which small populations could retain variation and inbreeding load. Multiple deleterious recessive mutations linked in repulsion generate pseudo-overdominance. Many tightly linked load loci could generate a balanced segregating load high enough to sustain ID over many generations. Such pseudo-overdominance blocks (or "PODs") are more likely to occur in regions of low recombination. They should also result in clear genetic signatures including genomic hotspots of heterozygosity; distinct haplotypes supporting alleles at intermediate frequency; and high linkage disequilibrium in and around POD regions. Simulation and empirical studies tend to support these predictions. Additional simulations and comparative genomic analyses should explore POD dynamics in greater detail to resolve whether PODs exist in sufficient strength and number to account for why ID and load persist within inbred lineages.

Potentially toxic elements in fen peatland soils located near lignite-fired power plants in Central Poland

The Grójec Valley (GV) peatland area in Central Poland is located close to lignite-fired power plants, which could be sources of potentially toxic elements (PTE). The aims of this study are: (1) to determine the effect of the lignite-fired power plants on soil pollution, (2) to evaluate pollution indices and magnetic susceptibility methods for determining the origin and distribution of PTE in soils, and (3) to demonstrate the importance of appropriate geochemical background (GB) selection for pollution studies in peatland soils. In order to comprehensively assess the soil pollution, four pollution indices (calculated using various types of GBs), and the mass-specific magnetic susceptibility method were used. The low content of analyzed PTE (Cd, Cr, Cu, Ni, Pb, Zn), the calculated pollution indices, and the magnetic susceptibility values (overall >20 × 10−8 m3 kg−1) indicated generally low pollution levels in the studied soils. This would suggest that power plants have had a minor impact on the fen soils, although exceptions were observed in the southernmost part of GV, the highest content of Cr (6.87–9.11 mg kg−1), Ni (7.11–10.3 mg kg−1) and Cu (14.1–19.5 mg kg−1). In addition, based on the Potential Ecological Risk (RI) and Contamination Security indexes (CSI), this area showed the highest potential ecological risk (81.9–102) and limit of toxicity (0.59–0.67) among the studied plots, respectively. The Enrichment factor (EF) and Contamination Security index (CSI) values were the most comparable, thus we consider that, in combination with magnetic susceptibility measurements, they comprise a useful set of tools for fen soil contamination studies. Furthermore, we suggest the application of an local organic GB (i.e. PTE content in the deeper organic layer) in such studies.

Population-specific causal disease effect sizes in functionally important regions impacted by selection

Many diseases exhibit population-specific causal effect sizes with trans-ethnic genetic correlations significantly less than 1, limiting trans-ethnic polygenic risk prediction. We develop a new method, S-LDXR, for stratifying squared trans-ethnic genetic correlation across genomic annotations, and apply S-LDXR to genome-wide summary statistics for 31 diseases and complex traits in East Asians (average N = 90K) and Europeans (average N = 267K) with an average trans-ethnic genetic correlation of 0.85. We determine that squared trans-ethnic genetic correlation is 0.82× (s.e. 0.01) depleted in the top quintile of background selection statistic, implying more population-specific causal effect sizes. Accordingly, causal effect sizes are more population-specific in functionally important regions, including conserved and regulatory regions. In regions surrounding specifically expressed genes, causal effect sizes are most population-specific for skin and immune genes, and least population-specific for brain genes. Our results could potentially be explained by stronger gene-environment interaction at loci impacted by selection, particularly positive selection.

Sex determination through X-Y heterogamety in Salix nigra.

The development of non-recombining sex chromosomes has radical effects on the evolution of discrete sexes and sexual dimorphism. Although dioecy is rare in plants, sex chromosomes have evolved repeatedly throughout the diversification of angiosperms, and many of these sex chromosomes are relatively young compared to those found in vertebrates. In this study, we designed and used a sequence capture array to identify a novel sex-linked region (SLR) in Salix nigra, a basal species in the willow clade, and demonstrated that this species has XY heterogamety. We did not detect any genetic overlap with the previously characterized ZW SLRs in willows, which map to a different chromosome. The S. nigra SLR is characterized by strong recombination suppression across a 2 MB region and an excess of low-frequency alleles, resulting in a low Tajima's D compared to the remainder of the genome. We speculate that either a recent bottleneck in population size or factors related to positive or background selection generated this differential pattern of Tajima's D on the X and autosomes. This discovery provides insights into factors that may influence the evolution of sex chromosomes in plants and contributes to a large number of recent observations that underscore their dynamic nature.

Introgression of "QTL-hotspot" region enhances drought tolerance and grain yield in three elite chickpea cultivars.

With an aim of enhancing drought tolerance using a marker-assisted backcrossing (MABC) approach, we introgressed the "QTL-hotspot" region from ICC 4958 accession that harbors quantitative trait loci (QTLs) for several drought-tolerance related traits into three elite Indian chickpea (Cicer arietinum L.) cultivars: Pusa 372, Pusa 362, and DCP 92-3. Of eight simple sequence repeat (SSR) markers in the QTL-hotspot region, two to three polymorphic markers were used for foreground selection with respective cross-combinations. A total of 47, 53, and 46 SSRs were used for background selection in case of introgression lines (ILs) developed in genetic backgrounds of Pusa 372, Pusa 362, and DCP 92-3, respectively. In total, 61 ILs (20 BC3 F3 in Pusa 372; 20 BC2 F3 in Pusa 362, and 21 BC3 F3 in DCP 92-3), with >90% recurrent parent genome recovery were developed. Six improved lines in different genetic backgrounds (e.g. BGM 10216 in Pusa 372; BG 3097 and BG 4005 in Pusa 362; IPC(L4-14), IPC(L4-16), and IPC(L19-1) in DCP 92-3) showed better performance than their respective recurrent parents. BGM 10216, with 16% yield gain over Pusa 372, has been released as Pusa Chickpea 10216 by the Central Sub-Committees on Crop Standards, Notification and Release of Varieties of Agricultural Crops, Ministry of Agriculture and Farmers Welfare, Government of India, for commercial cultivation in India. In summary, this study reports introgression of the QTL-hotspot for enhancing yield under rainfed conditions, development of several introgression lines, and release of Pusa Chickpea 10216 developed through molecular breeding in India.

Tai Tam Tuk reservoir dam in Hong Kong: historical background and site selection

Since 1842, the Hong Kong Colonial Government has been plagued with the perennial problem of deficiency in freshwater provision for an ever-growing population. A long-term solution to this was the start of the Tai Tam Waterworks Scheme on Hong Kong Island, with the Tai Tam Tuk reservoir dam, constructed between 1912 and 1917, being its largest and latest addition. This study drew its inspiration from a field trip during which the research team encountered several peculiar brick wells at Tai Tam Harbour. Driven by curiosity to learn their actual function, the team gleaned bits and pieces of archives scattered in Hong Kong and London, followed by in-depth interviews with senior residents nearby and a field study cum diving expedition in search of the remnants associated with the dam construction. Years of extensive research have paid off and led to the unveiling of the interlocking history of the wells with the Tai Tam Tuk reservoir. The findings contribute to a better understanding of the Tai Tam Tuk reservoir dam through a reconstruction of its history and an analysis of its site investigation process. The century-old remains of ground investigation constitute an illuminating testament to Hong Kong’s waterworks for engineers to understand time-tested engineering methodology.