Parental Lines Research Articles

QTL Mapping of Yield-Related Traits in Tetraploid Wheat Based on Wheat55K SNP Array.

To enhance the understanding of yield-related traits in tetraploid wheat, it is crucial to investigate and identify genes that govern superior yield characteristics. This study utilized the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line (RIL) population consisting of 120 lines developed through the crossbreeding of two tetraploid wheat varieties, Qin Hei-1 (QH-1) and Durum Wheat (DW). An investigation and analysis were conducted on 11 yield-related traits, including peduncle length (PL), neck length (NL), spike length (SL), flowering date (FD), heading date (HD), thousand-kernel weight (TKW), kernel area ratio (KAR), kernel circumference (KC), kernel length (KL), kernel width (KW), and kernel length-width ratio (KL-WR), over a period of three years in two locations, Yang Ling, Shaanxi, and Lin He, Inner Mongolia. The analysis identified nine stable loci among eight agronomic traits, named QSL.QD-1A.1, QNL.QD-4B.2, QPL.QD-4B.1, QFD.QD-2B, QHD.QD-2B.1, QHD.QD-4B, QKC.QD-4B.2, QKL-WR.QD-4B.6, and QKL.QD-4B.2. Among them, the additive effects of three QTLs, QSL.QD-1A.1, QNL.QD-4B.2, and QFD.QD-2B, were positive, indicating that the enhancing alleles at these loci were derived from the parent line QH-1. These three QTLs showed significant positive effects on the phenotypes of the population materials. Furthermore, potential functional genes were identified within the mapping intervals of QSL.QD-1A.1 and QNL.QD-4B.2, which regulate the development of spike length and neck length, respectively. These results provide potential QTLs and candidate genes, which broaden the genetic basis of agronomic traits related to yield, such as SL, NL, PL, and FD, and benefits for wheat breeding and improvement.

Genetic Variability for Root and Shoot Morpho-physiological Traits Contributing to Seedling Drought Stress Tolerance in Parental Lines of Pearl Millet

Drought stress severely affects plant growth and development leading to substantial reduction in yield and biomass accumulation. Forty one Pearl millet parental lines were subjected to seedling drought stress and morpho–physiological attributes along with individual drought stress response indices were recorded. Significant genetic variability existed for all the traits and genotype ICMX 1410698-SB-11-1-1-2(B) ranked first based on combined drought stress response index. Principal component analysis indicated that first two PCs explained 86.4% of variation under drought conditions. GCV ranged from 13.84 to 23.47% under drought indicating genetic basis for variability. D2 statistics grouped the genotypes into seven clusters. The maximum inter-cluster distance was reported between the clusters III and VII while clusters III & I ranked second under drought stress. These are potential drought tolerant parental lines for hybrid breeding. Root/Shoot ratio has been the major contributor for genetic divergence under both control and drought stress.

Breeding value of potato hybrid clones from the VIR collection revealed in the environments of Kamchatka Territory

Background. Potato breeding involves planned artificial hybridization between previously selected parental lines. A way to make potato breeding more efficient is to use the diversity of the germplasm and broaden the gene pool of parental lines. Interspecific potato hybrids originated on the elite potato germplasm display a set of valuable traits. The current challenge is to assess the performance of potato hybrids under specific soil and climate conditions to clarify their breeding value.The objective of the study was to evaluate potato hybrids in the environments of Kamchatka Territory according to a set of traits, identify the best parental lines, develop new hybrid combinations, and select promising breeding material.Materials and methods. Eleven potato hybrids from VIR were studied over three years (2020–2022) in the fields of Kamchatka Research Institute of Agriculture. The hybrids were benchmarked against two reference potato cultivars, ‘Fresco’ and ‘Vulkan’, belonging to the early and mid-early maturity groups, respectively. Crosses between the hybrids and 28 potato cultivars were carried out in the greenhouse. The new hybrid material was tested in a preliminary trial nursery for yield and earliness.Results. Hybrid 117-2 was better in yield (899 g/plant) than cvs. ‘Vulkan’ and ‘Fresco’ (700–739 g/plant). Hybrids 94-5, 99-10- 1, 8-1-2004, 8-3-2004, 8-5-2004, 135-3-2005, 135-5-2005, 99-6-6, and 134-2-2006 in most traits matched the potato cultivars, manifesting good berry formation and seed setting when crossed. Out of 140 crosses between 11 hybrids and 28 cultivars, 35 crosses between 10 hybrids and 13 cultivars were successful. Most hybrids were effectively used in crossings as maternal forms.Conclusion. VIR’s hybrids 94-5, 8-1-2004, and 8-5-2004 proved the most promising as source material for the development of new early potatoes under the conditions of Kamchatka Territory.

Abstract PO1-24-08: Targeting of HER3 potentiates the antitumor activity of paclitaxel against triple negative breast cancer

Abstract Background: Triple negative breast cancer (TNBC) is characterized by the absence of expression of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) overexpression. This aggressive form of breast cancer carries a higher risk of recurrence compared to other subtypes, presenting a significant clinical challenge. Although chemotherapy is commonly used as the primary treatment for a substantial number of TNBC patients, it is often accompanied by drug resistance and frequent tumor recurrence. Urgent efforts are needed to identify novel molecular targets specific to TNBC and develop effective therapies to combat this aggressive disease. The ultimate objective is to discover treatments capable of overcoming drug resistance and improving the overall survival of patients with TNBC. Methods: Immunohistochemistry was performed to examine the expression of HER3 in TNBC samples. Western blots were used to assess protein expression and activation. Cell proliferation and viability were determined by cell growth (MTS) assays. TCGA databases were analyzed to correlate HER3 mRNA expression with the clinical outcomes of TNBC patients. Specific shRNA was used to knockdown HER3 expression. LIVE/DEAD Cell Imaging was to detect live and dead cells. Orthotopic tumor models were established in nude mice to determine the capability of TNBC cells forming tumors and to test if our newly developed anti-HER3 monoclonal antibody (mAb) 4A7 could potentiate the antitumor activity of paclitaxel in vivo. Results: The chemo-resistant subline HCC1806-TR was obtained by subjecting TNBC HCC1806 cells to prolonged treatment with paclitaxel. In comparison to the parental cell line HCC1806-P, HCC1806-TR exhibited enhanced HER3 expression and activation. It is noteworthy that approximately half of the tested TNBC specimens and cell lines displayed elevated expression of HER3. Analyzing TCGA databases revealed that TNBC patients with high levels of HER3 mRNA expression in their tumors had significantly poorer overall survival (OS) and relapse-free survival (RFS) compared to those with low HER3 expression. Specifically knockdown of HER3 markedly inhibited TNBC cell proliferation and mammosphere formation in vitro and tumor growth in vivo. Blockade of HER3 signaling with our mAb (4A7) in combination with paclitaxel exerted significant antitumor activity against TNBC in vitro and in vivo. Conclusions: Our data demonstrate that increased HER3 is an effective therapeutic target for TNBC and our anti-HER3 mAb (4A7) may enhance the efficacy of paclitaxel in TNBC. Keywords: HER3, Anbibody, Chemotherapy, Triple Negative Breast Cancer Citation Format: Hui Lyu, Sanbao Ruan, Congcong Tan, Ann Thor, Bolin Liu. Targeting of HER3 potentiates the antitumor activity of paclitaxel against triple negative breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-24-08.

Abstract PO5-23-08: Adenylosuccinate lyase is essential for proliferation and mitochondrial function of endocrine therapy resistant breast cancer cells

Abstract Eighty percent of breast cancers express estrogen receptor alpha (ERα, ESR1) at the time of diagnosis. Endocrine therapy (ET) is the standard treatment that either block estrogen mediated ER activation (such as tamoxifen, fulvestrant) or suppress estrogen synthesis (such as exemestane, letrozole, or anastrozole). While ET is initially effective, emergence of ET-resistance is common and possess a major clinical challenge. Hence, there is an ongoing need to develop new treatments for ET-resistant-ERα positive breast cancer. In this study we investigated the role of adenylosuccinate lyase (ADSL), an enzyme of the de-novo purine biosynthesis pathway as a potential target of ET-resistant breast cancer. The protein level of ADSL in two independent ET-resistant cell line model LCC9 and T47D-4HT cells were significantly higher in comparison to its parental ET-sensitive cell lines, MCF7 and T47D cells, respectively. Transient knockdown of ADSL using two independent siRNA in both LCC9 and T47D-4HT cells results in a significant decrease of cell growth, colony, and spheroid formation. Notably, reduced ADSL levels in LCC9 cells prevented the cells from progressing from G1 to S phase of cell cycle with concurrent elevation of cyclin D1/D3, CDK2/4, and cyclin E. On the other hand, in T47D-4HT cells, ADSL reduction caused cells to accumulate in S-phase of cell cycle and showed lower levels of total cyclin D1 protein. Mechanistically, in LCC9 cells (but not in T47D-4HT cells), ADSL depletion induced DNA replication stress which activates (phosphorylate) ataxia-telangiectasia-mutated-and-Rad3-related kinase (ATR) and its major downstream effector checkpoint kinase 1 (Chk1) that in turn failed to de-phosphorylate the inhibitory-phospho-groups of cyclin-dependent kinase 2 (CDK2). In addition, ADSL depletion perturbed the mitochondrial function in both LCC9 and T47D-4HT cells. Oxygen consumption rate (OCR) and extracellular acidification rate (ECAR) was lower in both the cells along with the mitochondrial membrane potential. Pertinently, lower concentration of AICAR (5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside), a product of ADSL enzyme function, partially rescued the cell growth and restored mitochondrial membrane potential in ADSL-depleted LCC9 cells. To further understand the global effects of ADSL depletion we performed RNA-sequencing of LCC9 and T47D-4HT cells after ADSL depletion and compared with respective control siRNA transfected cells followed by gene set enrichment analysis. Intriguingly, diverse effect was observed in LCC9 and T47D-4HT cells as very few genes were found to be commonly regulated between these two cell lines. Analysis of clinical data sets revealed high level of ADSL transcript was associated with adverse progression free survival and overall survival in breast cancer patients treated with endocrine therapies. Overall, our findings demonstrate that ADSL-mediated de novo purine synthesis is critical for cellular growth, proliferation, and mitochondrial function of endocrine therapy-resistant breast cancer cells. Therefore, targeting ADSL is a novel potential therapeutic approach for ERα positive ET- resistant breast cancer. Citation Format: Anil Yadav, Lu Jin, Robert Clarke, Surojeet Sengupta. Adenylosuccinate lyase is essential for proliferation and mitochondrial function of endocrine therapy resistant breast cancer cells [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-23-08.

Abstract PO5-27-09: Pharmacological eIF4E inhibition suppresses anti-tumor activity in ER+ breast cancer

Abstract Elevated levels of eukaryotic initiation factor 4E (eIF4E) are found in a broad range of cancers, including breast, and have been associated with aggressive, drug resistant tumors. Furthermore, elevated eIF4E activity is sufficient to cause transformation in various cancers, while inhibition suppresses tumor growth. eIF4E, the main regulator and rate limiting factor of protein synthesis, is the downstream integrator of several important oncogenic signaling pathways (PI3K/AKT/mTOR, Ras/Raf/MEK, and Myc). Activation of eIF4E results in increased protein levels of key proliferation and metabolism proteins such as Cyclin D1 (CCND1) and Ornithine Decarboxylase 1 (ODC1), as well as an overall increase in cellular synthesis machinery, causing cellular growth and proliferation. Here, we describe the development and characterization of novel, potent, and selective eIF4E inhibitors. Compounds from this chemical series have nanomolar activity in multiple biochemical and biophysical m7G cap-competition assays as well as potent inhibition of translation in cellular and biochemical assays. In cells, these compounds rapidly and reversibly decrease protein levels of several oncogenes, including CCND1, leading to a G1 cell cycle arrest. We demonstrate that eIF4E inhibitors cause growth inhibition in a variety of breast cancer cell lines, including ER+ breast cancer. These inhibitors also inhibit growth of breast cancer lines with acquired resistance to Palbociclib with the same potency as the parental cell lines. Additionally, eIF4E inhibition shows an increased sensitivity in resistant cell lines when combined with standard of care (SOC), including Palbociclib. Select analogs from the series demonstrate favorable ADMET/PK properties with good oral bioavailability and low safety risk. Lastly, these compounds have demonstrated near complete tumor growth inhibition in non-breast cancer in vivo models. Ongoing experiments will address in vivo efficacy in ER+ breast cancer in both monotherapy and in combination with SOC. Citation Format: Matthew Friedersdorf, Devon Blake, Sarah Thompson, Krista Marran, Jessica Sorrentino. Pharmacological eIF4E inhibition suppresses anti-tumor activity in ER+ breast cancer [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO5-27-09.

Identification of low phosphorus tolerant parental lines of hybrid rice based on stress indices and haplotype analysis using Pup1 linked markers

Identification of low phosphorus tolerant parental lines of hybrid rice based on stress indices and haplotype analysis using Pup1 linked markers

Evaluation of combining ablity in isabgol through line X tester analysis

The present study was undertaken in three distinct environments (E1, E2, and E3) during the Rabi season of 2022-2023 in Rajasthan. The experimental set comprised of 70 genotypes, including 19 parents, 48 crosses, and 3 checks (Niharika, VI-3, GI-2), which were assessed using a randomized block design with three replications. The analysis of variance for combining ability revealed significant effects due to lines, testers, and line x tester interactions across all three environments, except for specific traits in certain environments. The parental lines L5, L10, and L7 demonstrated good general combining ability (GCA) effects across various traits. The specific combining ability (SCA) effects were diverse, with several crosses displaying consistently high effects, particularly for seed yield per plant, where crosses such as L11 x T3, L16 x T1, L6 x T2, L10 x T2, and L7 x T1 exhibited the highest estimates. Overall, the study provides valuable insights into the combining ability of Isabgol genotypes and their performance across different environments, contributing to the understanding of traits and potential breeding strategies.

Effects of row ratio and plant spacing for enhancing hybrid rice seed production in the tropics

The seed yield production determines the success of the development of hybrid rice. Here, an effective and efficient cultivation technology for producing hybrid rice seeds is optimized through spacing and row ratio management. This study aimed to evaluate the effects of spacing and row ratio of restorer (R) : CMS (A) on F1 hybrid rice seed production. The experiment was conducted at the Indonesian Center of Rice Research's experimental field in the dry season of 2016, using parental lines HIPA18 hybrid rice, i.e., CMS: IR79156A line and Restorer: IR53942 line. The experiment was laid out in a strip-plot design replicated three times. Two factors were studied, i.e., plant spacing between CMS lines and row ratio R by A-lines. The results indicated that the highest HIPA18 seed production was obtained from 20 cm x 20 cm spacing of CMS with row ratio 2R:14A, i.e., 3.62 tons ha-1. Plant spacing and row ratio interactions were improved tillers number per plant of restorer and F1 seed yields. Keywords: A-lines; CMS; F1 hybrid rice; R-lines

Strand-Specific RNA Sequencing Reveals Gene Expression Patterns in F1 Chick Breast Muscle and Liver after Hatching.

Heterosis refers to the phenomenon where hybrids exhibit superior performance compared to the parental phenotypes and has been widely utilized in crossbreeding programs for animals and crops, yet the molecular mechanisms underlying this phenomenon remain enigmatic. A better understanding of the gene expression patterns in post-hatch chickens is very important for exploring the genetic basis underlying economically important traits in the crossbreeding of chickens. In this study, breast muscle and liver tissues (n = 36) from full-sib F1 birds and their parental pure lines were selected to identify gene expression patterns and differentially expressed genes (DEGs) at 28 days of age by strand-specific RNA sequencing (ssRNA-seq). This study indicates that additivity is the predominant gene expression pattern in the F1 chicken post-hatch breast muscle (80.6% genes with additivity) and liver (94.2% genes with additivity). In breast muscle, Gene Ontology (GO) enrichment analysis revealed that a total of 11 biological process (BP) terms closely associated with growth and development were annotated in the identified DEG sets and non-additive gene sets, including STAT5A, TGFB2, FGF1, IGF2, DMA, FGF16, FGF12, STAC3, GSK3A, and GRB2. Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation presented that a total of six growth- and development-related pathways were identified, involving key genes such as SLC27A4, GLUL, TGFB2, COX17, and GSK3A, including the PPAR signaling pathway, TGF-beta signaling pathway, and mTOR signaling pathway. Our results may provide a theoretical basis for crossbreeding in domestic animals.

Elucidating the phenotypic basis of multi-environment stability for fiber yield and quality traits of cotton (Gossypium hirsutum L.) using 498 recombinant inbred lines

Understanding genotype-environment interactions and trait relationships is pivotal for guiding breeding efforts aimed at stabilizing cotton varieties across diverse environments while boosting yield and fiber quality. The study aimed to assess genotypic variability and stability in 10 agronomic and fiber quality traits across four environments (Anyang in 2020 and 2021 and Weixian in 2020 and 2021) for three parental lines (ZR014121, CCRI60, and EZ60) and their corresponding 498 recombinant inbred lines (RILs) populations. The results indicated that the analysis of variance showed significant genotype and genotype-by-environment effects for all measured traits. Analysis of correlation revealed highly significant positive correlations between seed cotton yield and each of boll weight (r = 0.95), lint yield (r = 0.90), and between boll weight and lint yield (r = 0.90), while highly significant negative correlations were noticed between fiber maturity and fiber elongation (r = −0.52) and between fiber length and lint percentage (r = −0.38). Furthermore, the weighted average of absolute scores (WAASB) was calculated for each trait, revealing moderate to high stability for some yield traits and fiber quality parameters. Also, the multi-trait stability index (MTSI) applied to these RILs populations identified G13 as the most stable line (MTSI = 5.5) and S23 as the least stable (MTSI = 12.1). Selecting 25 RILs with the lowest MTSI values (5.5–6.47) revealed elite stable lines with favorable trait values, providing a valuable genetic resource for developing high-performance cotton cultivars in diverse environments.

A novel four‐gene‐based inheritance model explains gradations of nakedness in cotton (Gossypium hirsutum L.)

AbstractIn crop improvement, delineating inheritance pattern of a character guides a plant breeder to choose appropriate breeding procedure, which enables ease of improving phenotypic expression of the traits. To deduce the inheritance pattern of naked seed or fuzzless character, four parental lines involving two purely naked seed types (DHN‐1 and DHN‐10), one partial naked seed type (SP46CC) and one fully fuzzy type (OSB415) were used to develop three different types of crosses, namely, naked × naked seed type cross (N × N), partial naked × naked seed type cross (PN × N) and fuzzy × naked seed type cross (F × N). We observed that naked trait segregates in the ratio of 11 naked: 5 partial naked in N × N cross, 22 naked: 42 partial naked in PN × N cross and 22 naked: 42 partial naked: 192 fuzzy in F × N cross. Our study reports a novel four‐gene model to understand inheritance nature of naked seed character where the presence of single basic dominant fuzzy gene negates the effect of genes controlling nakedness resulting fuzzy phenotype irrespective of the number of partial fuzzyness/nakedness imparting alleles. This indicates that nakedness is recessive to fuzzyness. Based on our results, we infer observing gradations of nakedness on seeds depends on the presence of number of partial fuzzyness imparting alleles, which led to a conclusion that the trait exhibited dose‐dependent expression with one basic gene for fuzziness.

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.

Identification of new lines resistance to blackleg in an Argentinian rapeseed-breeding program

Rapeseed (Brassica napus L.) is the third most important oil crop worldwide and it has a high demand for its industrial characteristics that make it suitable for human consumption and production of biofuels. The main yield losses of the crop are produce by blackleg, caused by Leptosphaeria maculans (Desmaz.) Ces. and of Not. [Anamorph Phoma lingam (Tode ex Fr.) Desmaz]. In this context, 469 inbred lines (ILs) of the INTA-EEA Paraná breeding program were phenotypic characterized for its resistance to Blackleg by artificial inoculations with a local isolation. From the initial 469 ILs, a total of 59 (13%) were identified as phenotypically resistant and were characterized by molecular makers associated to resistant genes (Rlm1, Lepr3, Rpg3Dun, and Rlm4) with the aim to identify lines carrying different resistance genes to be selected as parental lines in the development of new resistant genotypes. Moreover, the resistant ILs were characterized for its agronomics performance, including yield; percentage of oil; and content of fatty acids, over two crop seasons (2018 and 2019). A Generalized Procrustes Analysis was conducted to correlate all the traits evaluated and identify elite lines. From the 59 resistants ILs, four lines were selected based on their high performances and multiple resistant gene combinations, as started lines to develop a pyramiding gene strategy. The selection of these elite lines to combine traditional breeding and gene-pyramiding based on MAS in our breeding program is a useful strategy to develop superior rapeseed genotypes.

Optimizing selection based on BLUPs or BLUEs in multiple sets of genotypes differing in their population parameters

Key messageSelection response in truncation selection across multiple sets of candidates hinges on their post-selection proportions, which can deviate grossly from their initial proportions. For BLUPs, using a uniform threshold for all candidates maximizes the selection response, irrespective of differences in population parameters.Plant breeding programs typically involve multiple families from either the same or different populations, varying in means, genetic variances and prediction accuracy of BLUPs or BLUEs for true genetic values (TGVs) of candidates. We extend the classical breeder's equation for truncation selection from single to multiple sets of genotypes, indicating that the expected overall selection response (ΔGTot)\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$({\\Delta G}_{{\ ext{Tot}}})$$\\end{document} for TGVs depends on the selection response within individual sets and their post-selection proportions. For BLUEs, we show that maximizing ΔGTot\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\Delta G}_{{\ ext{Tot}}}$$\\end{document} requires thresholds optimally tailored for each set, contingent on their population parameters. For BLUPs, we prove that ΔGTot\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$${\\Delta G}_{{\ ext{Tot}}}$$\\end{document} is maximized by applying a uniform threshold across all candidates from all sets. We provide explicit formulas for the origin of the selected candidates from different sets and show that their proportions before and after selection can differ substantially, especially for sets with inferior properties and low proportion. We discuss implications of these results for (a) optimum allocation of resources to training and prediction sets and (b) the need to counteract narrowing the genetic variation under genomic selection. For genomic selection of hybrids based on BLUPs of GCA of their parent lines, selecting distinct proportions in the two parent populations can be advantageous, if these differ substantially in the variance and/or prediction accuracy of GCA. Our study sheds light on the complex interplay of selection thresholds and population parameters for the selection response in plant breeding programs, offering insights into the effective resource management and prudent application of genomic selection for improved crop development.

Assessment of Allelopathic Potential of Cotton Chromosome Substitution Lines.

Weed interference consistently poses a significant agronomic challenge in cotton production, leading to unfavorable direct and indirect consequences. Consequently, the predominant strategy employed to manage weeds is the application of synthetic herbicides. However, this extensive reliance has resulted in the development of herbicide-resistant weed populations due to the prolonged use of a single herbicide and the lack of rotation. This project focused on identifying weed-suppressive cotton chromosome substitution (CS) lines. These CS lines closely resemble the parent TM-1, an upland cotton derivative (Gossypium hirsutum). Each CS line carries a single chromosome or chromosome arm exchanged from G. barbadense, G. tomentosum, or G. mustelinum within the TM-1 background. In a greenhouse experiment utilizing a stepwise approach, five CS lines, along with two conventional varieties (Enlist and UA48) and the parent line (TM1), were assessed to determine their potential for suppressing Palmer amaranth growth. The plant height was measured 7, 14, and 21 days after establishment, and the chlorophyll content was measured 21 days after establishment. The results revealed varying levels of chlorophyll reduction in Palmer amaranth, with the Enlist variety displaying the lowest reduction (32%) and TM-1 exhibiting the highest (78%). Within 14 days of establishment, the CS lines T26lo, BNTN 1-15, and T11sh demonstrated substantial suppression of Palmer amaranth height, with reductions of 79, 70, and 71%, respectively. Conversely, Enlist displayed the least effective performance among the CS lines. Moreover, CS22, CS49, CS50, CS34, UA48, and CS23 displayed a decreasing trend in reducing Palmer amaranth height from 14 to 21 days after establishment. This research demonstrates the inherent herbicidal attributes within cotton CS lines against Palmer amaranth. In light of the versatile applications of cotton fibers and the unique characteristics of the G. hirsutum genome, this study investigates the potential of specific cotton lines in enhancing weed management practices. By elucidating the implications of our findings, we aim to contribute to promoting sustainability and developing alternatives to synthetic herbicides in agricultural systems.

Abstract P09: AN EX-VIVO COMBINATION DRUG SENSITIVITY PLATFORM FOR PREDICTING SENSITIVITY TO FLT3 INHIBITOR-BASED COMBINATION IN ACUTE MYELOID LEUKEMIA

Abstract FMS-like tyrosine kinase-3 (FLT3) mutations are often linked with poor prognosis in Acute myeloid leukemia (AML). Despite increasing availability of targeted therapy, such as FLT3 inhibitors (FLT3i), remission is often short-term and followed by relapse and drug resistance. With varying response rates to standard treatments, the need to understand the molecular mechanisms driving drug resistance and accurately predict responses to treatment is crucial. Here, we present the ability of Quadratic phenotypic optimization platform (QPOP), in accurately identifying potential responders to possible combination therapies in AML. AML cell lines and AML patient samples were treated with a set panel of drugs including FLT3i. QPOP drug combination scores and ranking were derived from cell viability response following treatment. 40 patients were recruited for the study, of which 20 patients were evaluated for their clinical concordance. RNA sequencing and molecular analysis was further conducted to determine the accuracy of QPOP predicted response and to determine mechanism of resistance to FLT3i. QPOP predicted response was concordant to patient treatment outcome with 80% sensitivity and specificity. QPOP analysis on AML cell lines accurately identified responders to FLT3i including the differential response between a FLT3- ITD isogenic parental and FLT3i resistant cell line. Serial QPOP analysis in a FLT3 mutant patient sample indicated a decrease in FLT3i sensitivity concordant with an increasing FLT3 allelic burden and the development of resistance. The development of resistance to FLT3i based combinations was correlated to an increase in phosphorylated AKT expression. Activation of AKT is associated with the upregulation of Forkhead box M1 (FoxM1) in the resistant cell line. Co-treatment with an AKT inhibitor restored sensitivity to FLT3i treatment in the resistant cells. We demonstrate that QPOP analysis accurately predicts sensitivity to drug-combinations and can be used as a tool to identify sensitivity to FLT3i-based combination therapy in AML. Citation Format: Noor Rashidha Bte Meera Sahib, Jen Wei Ying, Melissa Ooi, Yen Lin Chee, Jayalakshmi, Jameelah Bte Sheik Mohamed, Masturah Rashid, Edward KH Chow. AN EX-VIVO COMBINATION DRUG SENSITIVITY PLATFORM FOR PREDICTING SENSITIVITY TO FLT3 INHIBITOR-BASED COMBINATION IN ACUTE MYELOID LEUKEMIA [abstract]. In: Proceedings of Frontiers in Cancer Science; 2023 Nov 6-8; Singapore. Philadelphia (PA): AACR; Cancer Res 2024;84(8_Suppl):Abstract nr P09.

PARP1 promotes EGFR-TKI drug-resistance via PI3K/AKT pathway in non-small-cell lung cancer.

Tyrosine kinase inhibitor (TKI) resistance is the main type of drug resistance in lung cancer patients with epidermal growth factor receptor (EGFR) mutations, but its underlying mechanism remains unclear. The purpose of this work was to investigate the mechanism by which PARP1 regulates EGFR-TKI resistance to identify potential targets for combating drug resistance. The GEO databases, TCGA databases, western blot and qPCR studies were used to investigate the expression of PARP1 in lung cancer cells and tissues and its correlation with the prognosis of lung cancer. The expression of PARP1 in lung cancer TKI resistant cell PC9-ER and TKI sensitive cell PC9 was analyzed by qPCR and western blot. After knocking down of PARP1, CCK-8 assays, colony formation, flow cytometry were used to investigate its impact on erlotinib sensitivity, cell survival, cell cycle, and apoptosis. RNA-seq was used to investigate the mechanism by which PARP1 participates in EGFR-TKI resistance, and the results were validated in vitro and in vivo studies. PARP1 was highly expressed in both lung cancer tissues and cells. Subsequently, increased PARP1 expression was observed in PC9-ER compared with its parental cell line. Knockdown of PARP1 increased erlotinib sensitivity, promoted cell apoptosis, and suppressed cell growth. RNA-seq and previous studies have shown that the PI3K/AKT/mTOR/P70S6K pathway is involved in PARP1-mediated TKI resistance, and these results were confirmed by Western blot in vitro and in vivo. PARP1 may serve as a potential therapeutic target for reversing EGFR-TKI resistance in NSCLC via the PI3K/AKT/mTOR/P70S6K pathway.

Heterosis of endophytic microbiomes in hybrid rice varieties improves seed germination.

Seed endophytic microbiomes are shaped by host and environmental factors and play a crucial role in their host growth and health. Studies have demonstrated that host genotype, including hybridization, affects seed microbiomes. Heterosis features are also observed in root-associated microbiomes. It remains unclear, however, whether heterosis exists in seed endophytic microbiomes and whether hybrid microbiota provide noticeable advantages to host plant growth, especially to seed germination. Here, we investigated the structure of seed endophytic bacterial and fungal communities from three hybrid rice varieties and their respective parents using amplicon sequencing targeting 16S rRNA and ITS2 genes. Heterosis was found in diversity and composition of seed endophytic microbiomes in hybrids, which hosted more diverse communities and significantly higher abundances of plant growth-promoting taxa, such as Pseudomonas and Rhizobium genera compared with their parental lines. Co-occurrence network analysis revealed that there are potentially tighter microbial interactions in the hybrid seeds compared with their parent seeds. Finally, inoculation of seed-cultivable endophytes, isolated from hybrids, resulted in a greater promotion of seed germination compared with those isolated from parent lines. These findings suggest that heterosis exists not only in plant traits but also in seed endophytic microbiota, the latter in turn promotes seed germination, which offers valuable guidance for microbiome-assisted rice breeding.IMPORTANCEGenetic and physiological changes associated with plant hybridization have been studied for many crop species. Still, little is known about the impact of hybridization on the seed microbiota. In this study, we indicate that hybridization has a significant impact on the endophytic bacterial and fungal communities in rice seeds. The seed endophytic microbiomes of hybrids displayed distinct characteristics from those of their parental lines and exhibited potential heterosis features. Furthermore, the inoculation of seed-cultivable endophytes isolated from hybrids exhibited a greater promotion effect on seed germination compared with those isolated from the parents. Our findings make a valuable contribution to the emerging field of microbiome-assisted plant breeding, highlighting the potential for a targeted approach that aims to achieve not only desired plant traits but also plant-beneficial microbial communities on the seeds.

Phenotypic plasticity of okra for yield and associated traits

Background: The genetic improvement of okra for the agro-ecological conditions requires adequate genetic background for understanding the inheritance of the traits and genetic control.Aim: To evaluate collection of okra accessions for their phenotypic plasticity and their relationships among tested accession.Setting: Field trail laid in a randomised complete block design of three replication.Methods: A total of 24 okra accessions were planted at Loskop Research Station in Limpopo province, South Africa, during the 2020 and 2021 cropping seasons.Results: The analysis of variance showed significant differences among the accessions for yield and related traits measured. The principal components analysis revealed 68.85% total variation. The genotypic coefficient of variance (GCV) was higher than phenotypic coefficient of variance (PCV) for all the measured parameters. The study revealed medium heritability for yield (33%), high (≥ 60%), for hundred-seed weight and number of fruits per plant. A positive significant correlation between grain yield and fruit yield per plant (r = 0.39) was observed.Conclusion: The study recommended accessions Acc No. 1859.2.3.1, Acc No. 1181.2.1.1 and Acc No. 1900.2.3.1 to be used as breeding lines in future okra breeding programme.Contribution: The accessions identified as potential parents for okra improvement programme, based on complementary agronomic traits could be used for direct cultivation by small-scale farmers and parental lines for breeding population.