QTL-seq for the identification of candidate genes for days to flowering and leaf shape in pigeonpea

To identify genomic segments associated with days to flowering (DF) and leaf shape in pigeonpea, QTL-seq approach has been used in the present study. Genome-wide SNP profiling of extreme phenotypic bulks was conducted for both the traits from the segregating population (F2) derived from the cross combination- ICP 5529 × ICP 11605. A total of 126.63 million paired-end (PE) whole-genome resequencing data were generated for five samples, including one parent ICP 5529 (obcordate leaf and late-flowering plant), early and late flowering pools (EF and LF) and obcordate and lanceolate leaf shape pools (OLF and LLS). The QTL-seq identified two significant genomic regions, one on CcLG03 (1.58 Mb region spanned from 19.22 to 20.80 Mb interval) for days to flowering (LF and EF pools) and another on CcLG08 (2.19 Mb region spanned from 6.69 to 8.88 Mb interval) for OLF and LLF pools, respectively. Analysis of genomic regions associated SNPs with days to flowering and leaf shape revealed 5 genic SNPs present in the unique regions. The identified genomic regions for days to flowering were also validated with the genotyping-by-sequencing based classical QTL mapping method. A comparative analysis of the identified seven genes associated with days to flowering on 12 Fabaceae genomes, showed synteny with 9 genomes. A total of 153 genes were identified through the synteny analysis ranging from 13 to 36. This study demonstrates the usefulness of QTL-seq approach in precise identification of candidate gene(s) for days to flowering and leaf shape which can be deployed for pigeonpea improvement.

Effects of Sowing Dates on Yield and Yield Components of Different Varieties of Wheat (Triticum aestivum L.) in Western Uttar Pradesh

An experiment was conducted during Rabi season (November-December) of 2018–19 to study the effect of three dates of sowing (26th November, 11th December and 25th December) on growth, yield attributes and yield of fivewheat varieties (HD-2967, HD-3086, WH-1105, PBW-343 and PBW-226) at Agricultural Research Farm of IFTM University, Moradabad (UP) India. The experiment was laid out in Factorial Randomized Design with two replications. Sowing was done at spacing of 22.5 cm in sandy loam soil. The observations were recorded on growth, flowering, maturity, yield and yield components. Analysis of variance showed the significant variations were observed for the characters viz. plant height, days to flowering, spikes per plant, days to maturity, grain yield, test weight, straw yield, biological yield and harvest index due to changing dates of sowing. However, varietal variations were recorded for plant height, days to flowering, spikes per plant, days to maturity and test weight. Wheat sown on 26th November recorded significant increase in plant height, tillers plant-1, spikes-1 plant, grain yield and straw yield over late sowing on 11th December and 25th December. There was no significant variation among varieties for yield and yield contributing traits such as grains spike-1, grain and straw yield. Significant interaction effects between dates of sowing and varieties were found for days to flowering which showed that the variety HD-2967 is as best wheat variety for early sown and PBW-226 for late sown conditions in order to obtain better returns.

Sensitivity analysis of the CROPGRO-Canola model in China: A case study for rapeseed

Increasing domestic rapeseed production is an important national goal in China. Researchers often use tools such as crop models to determine optimum management practices for new varieties to increased production. The CROPGRO-Canola model has not been used to simulate rapeseed in China. The overall goal of this work was to identify key inputs to the CROPGRO-Canola model for calibration with limited datasets in the Yangtze River basin. First, we conducted a global sensitivity analysis to identify key genetic and soil inputs that have a large effect on simulated days to flowering, days to maturity, yield, above-ground biomass, and maximum leaf area index. The extended Fourier amplitude test method (EFAST) sensitivity analysis was performed for a single year at 8 locations in the Yangtze River basin (spatial analysis) and for seven years at a location in Wuhan, China (temporal analysis). The EFAST software was run for 4520 combinations of input parameters for each site and year, resulting in a sensitivity index for each input parameter. Parameters were ranked using the top-down concordance method to determine relative sensitivity. Results indicated that the model outputs of days to flowering, days to maturity, yield, above-ground biomass, and maximum leaf area index were most sensitive to parameters that affect the duration of critical growth periods, such as emergence to flowering, and temperature response to these stages, as well as parameters that affect total biomass at harvest. The five model outputs were also sensitive to several soil parameters, including drained upper and lower limit (SDUL and SLLL) and drainage rate (SLDR). The sensitivity of parameters was generally spatially and temporally stable. The results of the sensitivity analysis were used to calibrate and evaluate the model for a single rapeseed experiment in Wuhan, China. The model was calibrated using two seasons and evaluated using three seasons of data. Excellent nRMSE values were obtained for days to flowering (≤1.71%), days to maturity (≤ 1.48%), yield (≤ 9.96%), and above-ground biomass (≤ 9.63%). The results of this work can be used to guide researchers on model calibration and evaluation across the Yangtze River basin in China.

Evaluation and genetic analysis of common bean genotypes (Phaseolus vulgaris L.) at Dibatie and Mandura, Northwestern Ethiopia

Assessing and understanding the variations existing in crops due to genetic composition and environmental variability is very important in order to exploit the genetic constitution of crop plants. To this aim, variability measures such as phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) are commonly used. Heritability and genetic advance are major concerns for common bean to identify important traits for common bean genetic improvement. The field experiment was conducted at Mandura and Dibatie research substations working with sixteen genotypes of the common bean during 2017/2018 in lattice design with three replications to evaluate the performance of common bean genotypes and estimate the genetic variability. Heritability and genetic advance were estimated in relation to yield and its component traits for future breeding programs. Combined analysis of variance across locations revealed highly significant variations among genotypes for all traits under study. The PCV ranged from 3.36% for days to flowering to 15.91% for a number of pods per plant while the GCV value ranged from 0.75% for days to flowering to 13.74% for the number of pods per plant. Broad sense heritability values ranged from 5.00% for days to flowering to 84.61% for a hundred seed weight. Generally, the result of the study showed that significant genetic variability among tested genotypes and a simple selection for effective improvement of these traits. Keywords: common bean, genetic variability, genetic advance, heritability

De novo SNP calling reveals the candidate genes regulating days to flowering through interspecies GWAS of Amaranthus genus

Amaranths serve as pseudo cereals and also as traditional leafy vegetables worldwide. In addition to high vigor and richness in nutrients, drought and salinity tolerance of amaranth makes it a promising vegetable to acclimatize to the effects of global climate change. The World Vegetable Center genebank conserves about 1,000 amaranth accessions and various agronomic properties of these accessions were recorded during seed regeneration over decades. In this study, we verified the taxonomic annotation of the germplasm based on a 15K SNP set. Besides, in the assumption that the yield components of grain amaranths are different from those of leaf amaranths, we observed that grain amaranths presented larger inflorescences and earlier flowering than leaf amaranths. Dual-purpose amaranth showed larger leaves than leaf amaranths and later flowering than grain amaranths, which seemed reasonable because farmers can harvest more leaves during the prolonged vegetable stage, which also provides recovery time to enrich grain production. Considering frequent interspecies hybridization among grain amaranth complex, we proposed an interspecies GWAS for days to flowering, identifying a AGL20/SOC1 homolog. Meanwhile, another GWAS using only A. tricolor accessions revealed six candidate genes homologous to lba1, bri1, sgs1 and fca. These homologous genes were involved in the regulation of flowering time in Arabidopsis. This study revealed the usefulness of genotypes for species demarcation in the genus Amaranthus and the potential of interspecies GWAS to detect QTLs across different species, opening up the possibility of targeted introduction of specific genetic variants into different Amaranthus species.

Evaluation of exotic oat (Avena sativa L.) varieties for forage and grain yield in response to different levels of nitrogen and phosphorous

A field experiment was conducted during the Rabi season 2017–2018 (October–March) at the University of Agriculture, Peshawar research farm to examine the influence of different nitrogen (N) and phosphorus (P) levels on two different oat varieties: Australian and Ukrainian. The treatments included control and three levels of nitrogen and phosphorus at 30, 60, and 90 kg ha−1. The treatments were arranged in randomized complete block design (RCBD) and replicated three times. The findings showed that the oat varieties were significantly different from one another in yield and yield parameters. The Australian variety recorded higher emergence (49 plants m−2), days to emergence (15 days), days to flowering (122 days), days to maturity (145 days), plant height (142.7 cm), number of leaves (6.03 leaves plant−1), number of tillers (92.2 tillers m−1), biological yield (8,179.2 kg ha−1), and grain yield (3,725.6 kg ha−1) than the Ukrainian variety. Similarly, different N and P levels, the maximum days to emergence, days to flowering, and days to maturity were recorded in a control plot. The application of 105 kg N + 90 kg P ha−1 was statistically similar to the application of 105 kg N + 60 kg P ha−1. Maximum emergence (60 plants m−2), number of leaves (7.0 leaves plant−1), plant height (118.6 cm), number of tillers m−1 (102.6), biological yield (9,687.5 kg ha−1), and grain yield (4,416.7 kg ha−1) were determined in Australian variety. Based on the findings of this study, the Australian variety performed better in terms of yield and yield components and the application of N and P fertilizers at the rate of 105 kg N + 60 kg P ha−1 produced the best results in both oat varieties.

ESTIMATION OF VARIABILITY ANALYSIS PARAMETERS FOR MAJOR GROWTH AND FLOWERING TRAITS OF Lilium leichtlinii var. maximowiczii GERMPLASM

This experiment was carried out to evaluate the Lilium leichtlinii var maximowiczii germplasm collected from the different natural habitats from all over Korea. In total 30 accessions were studied for nine traits viz. plant height, leaf length, leaf width, the numbers of flowers, flower diameter, length of outer tepal, width of outer tepal, the number of leaf burn, and days to flowering in randomized block design with three replications. The ANOVA revealed highly significant variability prevailing among the investigated genotypes for almost all studied traits (except leaf width). The higher estimated value of GCV, PCV, heritability (H2), and genetic advance as percent of the mean was obtained for the number of flowers and leaf burn. The moderate to high GCV and PCV coupled with higher heritability estimates (H2) and GAM were found for plant height and flower diameter. Progeny selection would be effective as the prevalence of additive gene effect for these traits. Besides, leaf width, leaf length, length of outer tepal, the width of outer tepal, and days to flowering traits were possessed moderate to low GCV and PCV value coupled with the moderate value of heritability estimate with the low level of GAM proved to be the prevalence of non-additive genetic effect thereby indicating the necessity of alternative breeding approach for these traits improvement and breeding scheme. For the former group of traits breeding hybridization and selection would be an effective method, and primarily mean performance of these traits would be very handy for the decision of selection.

Identification of stable heat tolerance QTLs using inter-specific recombinant inbred line population derived from GPF 2 and ILWC 292

Heat stress during reproductive stages has been leading to significant yield losses in chickpea (Cicer arietinum L.). With an aim of identifying the genomic regions or QTLs responsible for heat tolerance, 187 F8 recombinant inbred lines (RILs) derived from the cross GPF 2 (heat tolerant) × ILWC 292 (heat sensitive) were evaluated under late-sown irrigated (January-May) and timely-sown irrigated environments (November-April) at Ludhiana and Faridkot in Punjab, India for 13 heat tolerance related traits. The pooled ANOVA for both locations for the traits namely days to germination (DG), days to flowering initiation (DFI), days to 50% flowering (DFF), days to 100% flowering (DHF), plant height (PH), pods per plant (NPP), biomass (BIO), grain yield (YLD), 100-seed weight (HSW), harvest index (HI), membrane permeability index (MPI), relative leaf water content (RLWC) and pollen viability (PV)) showed a highly significant difference in RILs. The phenotyping data coupled with the genetic map comprising of 1365 ddRAD-Seq based SNP markers were used for identifying the QTLs for heat tolerance. Composite interval mapping provided a total of 28 and 23 QTLs, respectively at Ludhiana and Faridkot locations. Of these, 13 consensus QTLs for DG, DFI, DFF, DHF, PH, YLD, and MPI have been identified at both locations. Four QTL clusters containing QTLs for multiple traits were identified on the same genomic region at both locations. Stable QTLs for days to flowering can be one of the major factors for providing heat tolerance as early flowering has an advantage of more seed setting due to a comparatively longer reproductive period. Identified QTLs can be used in genomics-assisted breeding to develop heat stress-tolerant high yielding chickpea cultivars.

Characterization of Oilseed Crop Noug (Guizotia abyssinica) Using Agro-Morphological Traits

Noug (Guizotia abyssinica) is an outcrossing oilseed crop that serves as a source of edible oil and other nutrients although its seed yield is generally low. The analysis of agro-morphological traits in relation to seed and oil yields is important for improving the productivity of this crop. The present study aimed at assessing the variation and heritability of quantitative (10) and qualitative (6) traits in noug based on 60 landrace accessions collected from wide geographic area in Ethiopia. The field trial was conducted at two sites in Ethiopia using a square lattice design. The analysis of variance revealed significant variation (p < 0.05) among these accessions. The highest broad-sense heritability (H2) was recorded for days to 10% flowering (DTF10; 85.4%), whereas number of capitula per plant (NCPP) and number of seeds per capitulum (NSPC) showed medium heritability (H2 = 38.5% and 31.6%, respectively). NCPP and NSPC showed a highly significant (p < 0.01) positive and negative genotypic correlation with days to flowering, respectively. These three traits showed very low genotypic coefficient of variation (<1%). In the case of qualitative traits, small capitulum, large flower, green leaf, green stem and course leaf margin showed significant association with higher number of seeds per plant (NSPP). Euclidean distance-based cluster analysis revealed that the clustering pattern of the accessions poorly correlates with the geographic distance between sample collecting sites. Similarly, no clear clustering pattern of accessions was revealed by principal component analysis (PCA) that explained 66.3% and 53.6% of the total variation of quantitative traits and qualitative traits, respectively. The oil content of these accessions was previously investigated and accessions with high oil content show large differences in terms of days to flowering, NSPP and thousand seed weight (TSW). Among the accessions included in this research, Hr_B21; Gj_C17, Sh_I4 and Gr_F15 Gj_G18 and Tg-R13 are top ranking, as they have at least one the following highly desirable traits: early maturity, high oil content, NSPP and TSW. Hence, crossbreeding of their selected genotypes would lead to the development of new cultivars that combine early maturity and both high seed and oil yields.