RNA-Seq analysis reveals potential salt- and drought stress tolerance-associated genes in advanced long-day onion breeding lines.

The development of advanced rice breeding lines and their evaluation for yield-attributes and salinity stress tolerance offers a significant opportunity to identify high-yielding salt-tolerant genotypes exhibiting desired traits. The present study aimed to examine the morpho-genetic variability of thirty-six advanced breeding lines of rice, with a focus on features that contribute to yield and salinity stress tolerance. Three replications of a randomized complete block design were used in the first experiment. Significant variability was observed among the lines for the studied quantitative traits. Based on yield attributing traits, the advanced breeding lines viz., Line 10, Line 21, Line 22, Line 23, Line 24 and Line 25 showed better performances in terms of earliness and yield. In yield-related variables such as the number of effective tillers per plant, plant height, and grain yield per plant exhibited high heritability coupled with high genetic advance as percentage of mean. The results of PCA biplot showed that the PC1 and PC2 accounted for the greatest variability of advanced Line 10, Line 11, Line 18, Line 21, Line 22, Line 23, Line 24, Line 25, Nerica 10, Begunipata, and Binadhan-14 with significant influence of the studied traits. Cluster analysis reflected that the high-yielding genotypes were placed in cluster II and VI. Highest genetic distance was observed among the genotypes of cluster III and cluster VI. In the second experiment, four advanced breeding lines along with salt tolerant and susceptible checks were assessed for salinity tolerance at the reproductive stage. The plants were cultivated in a large plastic-tub filled with field soil. During the late booting stage, saline (EC=10 dS/m) irrigation water was applied to the plants and continued for three weeks. While Lines 10 and 12 demonstrated a reduced decline, salt stress caused a significant loss in yield and yield-attributing characteristics in all genotypes. Line 10 and Line 12 which showed a reasonable degree of salt tolerance as well as early maturity were placed in the respective quadrant of the biplot. Stress tolerance indices also reflecting the better salt tolerance phenomena of the advanced Line 10 and Line 12. Considering all of the traits, Line 10 and Line12 could be selected as desired advanced rice lines for the development of early, high-yielding and salt tolerant rice varieties.

Assessment of genetic diversity among Pakistani wheat (Triticum aestivum L.) advanced breeding lines using rapd and sds-page

Variety adaptation to future climate for wheat is important but lacks comprehensive understanding. Here, we evaluate genetic advancement under current and future climate using a dataset of wheat breeding nurseries in North America during 1960-2018. Results show that yields declined by 3.6% per 1 °C warming for advanced winter wheat breeding lines, compared with −5.5% for the check variety, indicating a superior climate-resilience. However, advanced spring wheat breeding lines showed a 7.5% yield reduction per 1 °C warming, which is more sensitive than a 7.1% reduction for the check variety, indicating climate resilience is not improved and may even decline for spring wheat. Under future climate of SSP scenarios, yields of winter and spring wheat exhibit declining trends even with advanced breeding lines, suggesting future climate warming could outpace the yield gains from current breeding progress. Our study highlights that the adaptation progress following the current wheat breeding strategies is challenging.

Genomic prediction is a promising approach for accelerating the genetic gain of complex traits in wheat breeding. However, increasing the prediction accuracy (PA) of genomic prediction (GP) models remains a challenge in the successful implementation of this approach. Multivariate models have shown promise when evaluated using diverse panels of unrelated accessions; however, limited information is available on their performance in advanced breeding trials. Here, we used multivariate GP models to predict multiple agronomic traits using 314 advanced and elite breeding lines of winter wheat evaluated in 10 site-year environments. We evaluated a multi-trait (MT) model with two cross-validation schemes representing different breeding scenarios (CV1, prediction of completely unphenotyped lines; and CV2, prediction of partially phenotyped lines for correlated traits). Moreover, extensive data from multi-environment trials (METs) were used to cross-validate a Bayesian multi-trait multi-environment (MTME) model that integrates the analysis of multiple-traits, such as G × E interaction. The MT-CV2 model outperformed all the other models for predicting grain yield with significant improvement in PA over the single-trait (ST-CV1) model. The MTME model performed better for all traits, with average improvement over the ST-CV1 reaching up to 19, 71, 17, 48, and 51% for grain yield, grain protein content, test weight, plant height, and days to heading, respectively. Overall, the empirical analyses elucidate the potential of both the MT-CV2 and MTME models when advanced breeding lines are used as a training population to predict related preliminary breeding lines. Further, we evaluated the practical application of the MTME model in the breeding program to reduce phenotyping cost using a sparse testing design. This showed that complementing METs with GP can substantially enhance resource efficiency. Our results demonstrate that multivariate GS models have a great potential in implementing GS in breeding programs.

Yellow rust of barley caused by Puccinia striiformis f. sp. hordei (Psh), is an important disease in barley growing regions of India and worldwide. For identifying adult plant stage resistance to yellow rust, a set of 29 barley advanced breeding lines was tested at five locations, Durgapura, Jammu, Ludhiana, Bajaura and Karnal during 2016-17 and 2017-18. The seedling resistance test was conducted on 27 barley advanced breeding lines against seven Psh pathotypes separately under controlled conditions at ICAR-IIWBR, Shimla during 2017-18. As consequences, seven lines (DWRFB10, DWRFB12, DWRFB14, DWRFB15, DWRFB19, DWRFB20, and DWRFB28) were found immune to highly resistant against yellow rust at adult plant stage across the locations. Similarly, seven advanced breeding lines viz., DWRFB11, DWRFB12, DWRFB13, DWRFB14, DWRFB19, DWRFB20, and DWRFB27, were found resistant to yellow rust at the seedling stage. On the basis of APR and SRT, four advanced barley breeding lines, DWRFB12, DWRFB14, DWRFB19 and DWRFB20 were highly resistant to yellow rust (nearly immune) both at seedling and adult-plant stages. DOI.org10.25174/2249-4065/2019/85076

Drought and phosphorus (P) deficiency stress are two significant natural abiotic stresses restricting rice growth and yield worldwide. Developing rice varieties tolerant to drought and low P stress is crucial for sustainable agricultural production. To address these issues, two separate experiments were conducted using selected advanced rice breeding lines to study the impact of drought and low P stress on yield-attributing traits. The first experiment evaluated the drought stress tolerance of five advanced lines (Lines 14, 16, 20, and 22) under pot culture conditions by applying drought stress and not providing water throughout the reproductive stages (late booting to ripening). All genotypes under study exhibited a significant reduction in the yield of grain, ranging from 75.68% to 39.52%, as well as spikelet fertility and SPAD value when drought stress was applied; however, Line 20, BRRI dhan71, and Nerica 10 showed a less significant decrease. Conversely, days to first flowering, days to maturity, and the number of unfilled grains increased significantly in all of the genotypes studied; however, Line 20, BRRI dhan71, and Nerica10 showed a slight increase. Based on stress tolerance indices, Nerica 10, BRRI dhan71, and Line 20 are the best performers. In the second experiment, four advanced lines (Lines 3, 4, 6, and 20) were evaluated for low phosphorus (P) stress tolerance under conditions where no P fertilizer was applied. The application of low P stress significantly harmed all of the yield characteristics (excluding days to first flowering, days to maturity, and number of unfilled grains) of most of the genotypes, while Binadhan-17, Line 4, and Line 20 displayed a milder reduction, with overall grain yield reductions across genotypes ranging from 40.74% to 8.78%. Binadhan-17 and Line 20 showed higher stress tolerance indices and were classified as low P-tolerant genotypes. Considering both experimental results, the advanced breeding Line 20 was categorized as a promising advanced line. Therefore, Line 20 could be a potential donor parent for breeding drought and P deficiency-tolerant rice varieties.

Verticillium wilt (VW), caused by Verticillium dahliae Kleb, is one of the most destructive diseases in cotton (Gossypium spp.). The most efficient and cost-effective method of controlling the disease is the use of resistant cotton cultivars. Most commercial cultivars and elite breeding lines are developed under non-VW conditions and their responses to the disease are currently unknown. This study was conducted to evaluate current commercial cotton cultivars and advanced breeding lines for VW resistance. In 2011–2013, a total of 84 cultivars from major US seed companies, 52 advanced breeding lines from the US public breeding programs, and 87 introgression lines from a cross between Acala 1517-99 × Pima PHY 76 from the New Mexico Cotton Breeding Program, were evaluated for VW resistance in the greenhouse. Cotton cultivars and breeding lines were evaluated in ten separate replicated tests by inoculation with a defoliating-type isolate of V. dahliae. While leaf severity rating and percentages of infected plants, infected leaves and defoliated leaves were found to be significantly and positively correlated with one another, leaf severity rating and percentage of infected leaves were best choices because of their relatively low coefficients of variation and higher resolutions to differentiate resistant genotypes from susceptible ones. The heritabilities for the VW resistance traits ranged from 0.58 to 0.80 with an average of 0.67, indicating that variation in VW resistance is predominantly due to genetic factors. Of the 223 commercial cultivars and advanced lines, six Upland cultivars (FM 9160B2F, FM 9170 B2F, NG 4010 B2RF, Nitro 44 B2RF, DP 1219 B2RF, and ST 4288 B2F), five advanced lines (Ark 0403-3, MD 10-5, MD 25ne, NC11AZ01, and PD 0504), two introgression lines from Upland × Pima (NM11Q1157 and 08N1618), and four Pima cultivars (COBALT, DP 357, PHY 800, and PHY 830) had higher levels of resistance to VW. The resistance shown by most of these cultivars in the greenhouse was consistent with their performance in previous field tests. Based on the initial VW resistance, 19 highly or moderately resistant genotypes were chosen for re-evaluation and 30 genotypes were also assessed more than once for VW resistance in different tests, most of which had concordant performance. These cultivars and advanced lines should be useful resources to improve VW resistance in cotton breeding.

The current study aimed to evaluate 200 advanced breeding lines along with three checks during kharif,2024 to delineate the extent of genetic diversity for yield and its component trait using multivariate techniques using Principal Component Analysis (PCA), Hierarchical clustering and correlation. In PCA, the principal components having eigen values greater than one viz., PC1, PC2, PC3,PC4 and PC5 detailing 20.3%, 16.7%, 14%, 12.8% and 12.7% respectively witha cumulative effect of 76.7% of the total variation. Based upon Wards method of hierarchical clustering, 200 rice advanced breeding lines along with three checks were divulged into 14 clusters based on different traits studied, in which cluster I topped with 30 advanced breeding lines followed by cluster XIII and VI with 29 and 25 advanced breeding lines, respectively. The advanced breeding linesconfined to cluster X registered higher cluster mean values for grain yield. Besides, cluster XIV showed highest values for panicle length, ear bearing tillers/m2 and grains per panicle. The trait grain yield registered positive association with days to 50 % flowering, days to maturity, ear bearing tillers/m2, grains per panicle and test weight through correlation analysis.From the present study, the advanced breeding lines viz., NDRA 78, NDRA 225, NDRA 226, NDRA 227 and NDRA 50 were identified as genetically potential advanced breeding lines for commercial exploitation for enhancing yield and component traits in rice.

Field evaluation for the combination of white mould and tomato spotted wilt disease resistance among peanut genotypes

Five advanced breeding lines of sweet potato were assessed for polyethylene glycol (PEG)-6000-mediated osmotic stress tolerance in vitro. Significant variation among the morphophysiological properties and antioxidative enzyme activities was observed under different levels of PEG (0, 0.1, and 0.2 MPa) incorporated in Murashige and Skoog (MS) medium. An induction of antioxidative enzymes-superoxide dismutase (SOD, Enzyme Commission [EC] 1.15.1.1), catalase (CAT, EC 1.11.1.6), ascorbate peroxidase (APX, EC 1.11.1.1), guaiacol peroxidase (GPX, EC 1.11.1.7), monodehydroascorbate reductase (MDHAR, EC 1.6.5.4), dehydroascorbate reductase (DHAR, EC 1.8.5.1), glutathione reductase (GR, EC 1.6.4.2), and polyphenol oxidase (PPO, EC 1.14.18.1)-was observed under stress compared to the control, and this induction was pronounced in the tolerant genotypes than in the susceptible ones. Among the antioxidant enzymes, CAT showed a strong positive correlation with GPX (Pearson's correlation coefficient [r] = 0.73), whereas MDHAR was strongly and positively correlated with APX (r = 0.73) and PPO (r = 0.68). A significant increase in antioxidative enzyme activities was associated with lower growth retardation, as evident from the correlation study. Genotypes SP-30, followed by SP-18, possessed high principal component (PC1) scores and were rich in antioxidative enzymes, whereas genotypes SP-24, SP-26, and SP-28 exhibited lower enzyme activities and skewed morphological traits. The overall pattern of osmotic stress tolerance among the tested advanced sweet potato breeding lines followed the order: SP-30 > SP-18 > SP-26 > SP-24 > SP-28. The outcome of the study encourages the advancement of SP-30 for inclusion in future breeding strategies and/or its release following the official variety release procedures.

Field resistance to cylindrocladium black rot and tomato spotted wilt virus among advanced runner-type peanut breeding lines

An investigation was conducted at Indian Institute of Rice Research (IIRR) farm located at Rajendranagar, Hyderabad. The experimental field was laid in RBD design using 30 advanced Breeding Lines ABL (SP-02, SP-03, SP-08, SP-13, SP-25, SP-34, SP-37, SP-55, SP-57, SP-61, SP-63, SP-69, SP-70, SP-72, SP-75, SP-80, SP-351, SP-352, SP-353, SP-354, SP-355, SP-356, SP-357, SP-358, SP-359, SP-360, NDR-359, IR-64 and JAYA), including one check variety BPT-5204.BPT-5204 used as quality check. For molecular characterization of advanced breeding lines seven genes (Gn1&Gn2for grain number; SCM2 and SCM3 for strong culm; Gs3for grain size; Gw5for grain weight; Spl14for spikelet length) and three QTLs (Yld12.1, Yld2.1 and Yld4.1for yield) were used. Upon genotyping, 30 advanced breeding lines, only one advanced breeding line SP-08 showed the presence of seven yield contributing genes/QTLs (Gn1, Gn2, SCM2, SCM3, Gw5, Yld12.1, Yld2.1) indicating presence of high potential for yield. Two advanced breeding lines showed the presence of six yield contributing genes/QTLs, they are SP-69 (Gn1, Gn2, SCM3, Gw5, Spl14, Yld2.1) and SP-70 (Gn1, SCM3, Gw5, Gs3, Yld2.1, Yld12.1). Whereas four advanced breeding lines showed the presence of five yield contributing genes. They are SP-37 (Gn2, SCM3, Gw5, Yld12.1, Yld2.1), SP-55 (Gn2, SCM2, SCM3, Gw5, Yld2.1), SP-75 (Gn1, Gn2, SCM3, Gw5, Yld12.1) and SP-61 (Gn1, Gn2, SCM2, Gw5, Yld2.1). The morphological and physiological parameters of advanced breeding lines were correlated with the molecular analysis. SP-08 showed better morphological and physiological parameters like number of tillers, LAD, LAI, CGR, NAR, and also showed the presence of seven (Gn1, Gn2, SCM2, SCM3, Gw5, Yld12.1 and Yld2.1) yield contributing genes/QTLs. Genotype, SP-70 showed better in several physiological parameters photosynthetic rate, SPAD meter readings, dry matter accumulation, and also contain six (Gn1, SCM3, Gw5, Gs3, Yld2.1 and Yld12.1) genes/QTLs. Genotype, SP-69 higher panicle length and also contain six corresponding genes governing (Gn1, Gn2, SCM3, Gw5, Spl14 and Yld2.1) genes/QTLs. Two advanced breeding lines namely SP-08, SP-70 can be further probed thoroughly for further increasing yield and yield attribute.

Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

The research work was conducted at Jute Agriculture Experimental Station (JAES) Manikganj and Jute Agriculture Regional Station (JARS) Faridpur of Bangladesh. The present study aimed at determining the nutritional requirement for optimum growth and yield of an advanced olitorius breeding line of O-0512-6-2 in Bangladesh. The experiment was laid out in RCBD with 10 treatments having three replications during the year 2019, 2020 and 2021. The results indicated significant effect on yield and yield contributing characters over control with different fertilizer (NPKS) levels of advanced olitorius breeding line of O-0512-6-2. The highest number of plant height, base diameter, green weight with leaves and without leaves was observed by the treatment T3 (N100P10K25S20) which is statistically significant. The highest fiber yield (2.75 t ha−1) and stick yield (6.50 t ha−1) at Manikganj and highest fiber yield (2.58 t ha−1) and stick yield (6.09 t ha–1) at Faridpur was also obtained by the combined dose of N100P10K25S20 (T3) kg ha−1. Therefore, this combination N100P10K25S20 Kg ha−1 seemed to be optimum for maximum growth and yield of advanced olitorius breeding line of O-0512-6-2. Bangladesh Agron. J. 2024, 26(2): 1-6

Background: Drought stress has a significant impact on groundnut (Arachis hypogaea L.) production, causing severe yield losses, especially in semi-arid regions. The development of drought-tolerant cultivars is important to reduce the adverse effect of water constraint on groundnut productivity. This study aimed to evaluate the agronomic performance of 17 advanced drought-tolerant groundnut breeding lines and a standard control variety, Werer- 961, under rainfed conditions at Pawe Agricultural Research Center (PARC), Ethiopia, during the 2022 and 2023 cropping seasons. Methods: The field experiment was conducted using a randomized complete block design (RCBD) with three replications over two consecutive years. The study evaluated 17 advanced groundnut breeding lines, including the standard check variety, Werer-961. Selection was based on their previously evaluated performance in drought-prone regions and demonstrated high yield potential under stress conditions. The chosen lines comprised both early- and late- maturing cultivars to assess their adaptability to varying drought intensities. Critical traits related to drought tolerance and yield potential in water-limited environments were recorded. Statistical analyses, including correlation analysis, histogram evaluation and Q-Q plot analysis, were performed to identify superior genotypes. Result: The experiment depicted significant variation of genotypes against all the important agronomic characteristics, such as days to emergence, days to maturity, pod yield, seed yield, pods per plant and seed weight. Several lines, including RDRGVT ICGV SM 01514, RDRGVT ICGV 14788 and RDRGVT ICGV 8540, exceeded the check variety based on pod and seed yield. The genotype-by-environment interaction was significant for pod quantity per plant and seed weight. Correlation research showed that pod number per plant was very significantly related to both pod yield and seed production. These results are important findings in the development of drought-tolerant groundnut cultivars that can produce well under stressful conditions in the rainfed agriculture of Ethiopia.