Genetic analysis and QTL mapping of early root bulking in an F1 population of non-inbred parents in cassava ( Manihot esculenta Crantz)

The genetic basis of early bulking in cassava was studied in a replicated, multi-locational trial using 144 F1 progeny derived from an intra-specific cross between two non-inbred parents. A second, sequential harvest experiment examined the relative importance of eight yield-related traits on early bulking and their QTLs during the crop growth cycle. Our objectives were to identify traits, and genes controlling them, strongly associated with early yield as a first step to marker-assisted improvement of the trait. Multiple linear regression analysis and stepwise regression of early yield on eight yield-related traits revealed harvest index, dry foliage weight and root diameter as the most important factors associated with early yield. A total of 18 QTLs controlling early yield were identified in the first and second experiments and 27 QTLs, 2 for dry foliage weight, 8 for harvest index and 17 for root diameter, in the second experiment. The individual effects of alleles at these QTLs identified ranged from 7% to 33% of the phenotypic variance explained. Seven of 18 QTLs found for early yield (39%) coincided with QTLs associated with one or more traits with significant influence on early yield. The results show that sink and source capacities are very important in determining early yield. The identification of a number of QTLs with positive effect for increased early yield provides an opportunity for marker-assisted selection and improvement of early bulking potential in cassava.     

Localization of quantitative trait loci (QTL) for agronomic important characters by the use of a RFLP map in barley (Hordeum vulgare L.)

Two hundred and fifty doubled haploid lines were studied from a cross between two 2-row winter barley varieties. The lines were evaluated for several characters in a field experiment for 3 years on two locations with two replications. From a total of 431 RFLP probes 50 were found to be polymorphic and subsequently used to construct a linkage map. Quantitative trait loci (QTLs) were determined and localized for resistance against Rhynchosporium secalis and Erysiphe graminis, for lodging, stalk breaking and ear breaking tendency, for the physical state before harvest, plant height, heading date, several kernel parameters and kernel yield. The heritability of the traits ranged from 0.56 to 0.89. For each trait except for kernel thickness, QTLs have been localized that explain 5–52% of the genetic variance. Transgressive segregation occurred for all of the traits studied.     

A triple test cross analysis to detect epistatic gene effects in cabbage (Brassica oleracea var. capitata L.): An updated methodology

The cross-pollinated crop Brassica oleracea var. capitata L. shows good heterotic heterosis at high output; better standing of the plants; early maturity; larger and more homogeneous heads; consistency of head compactness; and disease-tolerance in F1 hybrids. There is very limited information documented on the epistasis of essential cabbage characters. We expand the research in this study to include an upgraded test to cross-design for enrolling and estimating epistasis and other genetic variance components controlling head yield and component traits in cabbage. The data was obtained from 45 families produced by crossing 15 lines with three testers; SC 2008–09, E-1-3-1&2, and their single cross F1, was subjected to triple test cross analysis. The current study results confirmed “j + 1” form of epistasis which is a major component for all traits. The plant spread, non-wrapper leaves, nethead/grossweight, polar/equatorial diameter, marketable head yield per plot, iron content and dry matter lugged both “j + 1” and 'i' type with the predominance of the 'i' type of interaction. Except for head shape index, equatorial diameter, head compactness was more noticeable when observed in dominance component. The degree of dominance is in the partial range, but both the head shape index/compactness and equatorial diameter showed over dominance. For maximum part, superiority was shown in both the directions. Appropriate breeding procedures are proposed to exploit the different forms of gene effects discovered for genetic improvement of head yield and quality traits.     

Genetic mapping of QTLs affecting productivity and plant architecture in a full-sib cross from non-inbred parents in Cassava (<Emphasis Type="Italic">Manihot esculenta</Emphasis> Crantz)

An attempt was made to identify quantitative trait loci (QTLs) for several productivity and plant architecture traits in a full-sib progeny of 144 individuals from two non-inbred parents in cassava. A molecular linkage map of this cross constructed previously with over 250 markers was the source of molecular markers. The progeny were grown under field conditions at two locations (Palmira and Quilichao) in Colombia and evaluated in 2 years (1998 and 1999) for architecture and productivity traits. Architecture traits evaluated were plant height (PH), branching height (BH), branching levels (BL), branching index (BI), stem portion with leaves (SPL) and leaf area index (LAI). Productivity traits were those related to total dry matter production and distribution, namely fresh root yield (FRY), fresh shoot yield (FSY), harvest index (HI) and the number of storage roots (NR). Phenotypic evaluation of the traits in this population revealed continuous variation for all traits. Broad-sense heritability estimates, ranged from 36% (for NR) to 94% (for BH). Several significant phenotypic correlations were observed between architecture and productivity traits. Primary QTLs, using the single-QTL model, and secondary QTLs, by a primary QTL interaction model, were detected by interval mapping. A total of 30 primary QTLs and 84 secondary QTLs were detected. We identified 35% of detected QTLs in two or more trials, the other QTLs were environment-specific. These results underscore the significant genotype × environment interactions found for most of the traits. Several genomic segments affecting multiple traits were identified and were in agreement with correlation among traits. All QTLs identified for FRY were found associated with either component traits of productivity or architecture traits. This study suggests that QTLs for plant architecture can be used to improve productivity. However an exhaustive search and analysis of QTLs controlling architecture is required before marker-assisted selection (MAS) for increasing productivity can be initiated.Communicated by H. C. Becker     

Genotypic variations in activities of phospho<Emphasis Type="Italic">enol</Emphasis>pyruvate carboxylase and correlations with leaf photosynthetic characteristics and crop productivity of cassava grown in low-land seasonally-dry tropics

Field trials with a large group of cassava germplasm were conducted at the seasonally-dry and hot environments in southwest Colombia to investigate photosynthetic characteristics and production under drought conditions. Measurement of net photosynthetic rate (P _N), photosynthetic nitrogen use efficiency (PNUE), mesophyll conductance to CO₂ diffusion (g _m), and phosphoenolpyruvate carboxylase (PEPC) activity of upper canopy leaves were made in the field. All photosynthetic characteristics were significantly correlated with final dry root yield (Yield). Correlations among the photosynthetic traits were also significant. PEPC activity was highly significantly correlated with P _N and PNUE, indicating the importance of the enzyme in cassava photosynthesis and productivity. Among a small selected group from the preliminary trial for yield performance, the second year Yield was highly significantly correlated with P _N measured on the first year crop. Thus variations in the measured photosynthetic traits are genetically controlled and underpin variations in yield. One short-stemmed cultivar M Col 2215 was selected for high root dry matter content, high harvest index, and tolerance to drought. It was tested under the semi-arid conditions of the west coast of Ecuador; participating farmers evaluated cultivar performance. This cultivar was adopted by farmers and officially released in 1992 under the name Portoviejo 650.     

Association between morphological traits and yield components in the durra sorghums of Ethiopia

The Ethio-Sudan region is recognized as the center of origin and diversity for cultivated sorghum. All major races of the crop are widely grown in Ethiopia with durras being dominant. The objective of the present study was to determine the extent of morphological variability among the Ethiopian durras and examine the pattern of relationships among these traits and their association with yield and yield components. Two hundred accessions collected from major sorghum-growing regions of the country were evaluated during the 2007 season at two locations representing hot and dry low land and mild mid-altitude environments. A randomized complete block design with three replications was used. Data were collected on phenology, plant height, a range of leaf traits and yield components. Significant variation was observed among all traits measured. Phenological traits and plant height were significantly correlated with each other and with all leaf traits. There was positive correlation among leaf traits, and between leaf traits and yield components except thousand kernel weight (TKW) and panicle length (PL). Grain fill duration was negatively correlated with all traits except days to maturity, TKW, and leaf length. Yield components except PL and TKW were positively correlated with each other. Selection that focuses on key yield components, larger leaf area, and on enhancing the grain filling rate by reducing excessive grain fill duration may contribute to yield improvement.     

Genetic Components of Heterosis for Seedling Traits in an Elite Rice Hybrid Analyzed Using an Immortalized F_2 Population

Utilization of heterosis has greatly contributed to rice productivity in China and many Asian countries. Superior hybrids usually show heterosis at two stages: canopy development at vegetative stage and panicle development at reproductive stage resulting in heterosis in yield. Although the genetic basis of heterosis in rice has been extensively investigated, all the previous studies focused on yield traits at maturity stage. In this study, we analyzed the genetic basis of heterosis at seedling stage making use of an "immortalized F2" population composed of 105 hybrids produced by intercrossing recombinant inbred lines(RILs) from a cross between Zhenshan 97 and Minghui 63,the parents of Shanyou 63, which is an elite hybrid widely grown in China. Eight seedling traits, seedling height, tiller number, leaf number, root number, maximum root length, root dry weight, shoot dry weight and total dry weight, were investigated using hydroponic culture. We analyzed single-locus and digenic genetic effects at the whole genome level using an ultrahigh-density SNP bin map obtained by population re-sequencing. The analysis revealed large numbers of heterotic effects for seedling traits including dominance, overdominance and digenic dominance(epistasis) in both positive and negative directions. Overdominance effects were prevalent for all the traits, and digenic dominance effects also accounted for a large portion of the genetic effects. The results suggested that cumulative small advantages of the single-locus effects and two-locus interactions, most of which could not be detected statistically, could explain the genetic basis of seedling heterosis of the F_1 hybrid.     

Epistasis plays an important role as genetic basis of heterosis in rice

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Economic injury levels for western flower thrips (Thysanoptera: Thripidae) on greenhouse cucumber

Low, medium and high densities of western flower thrips, Frankliniella occidentalis (Pergande), were established in three greenhouses at the Greenhouse and Processing Crops Research Centre, Ontario, Canada, in 1996 and 1998 to develop economic injury levels for thrips on greenhouse cucumber. Thrips densities were monitored weekly using yellow sticky traps and flower counts. Fruit was harvested twice a week, graded for size, weighed, and rated for thrips damage using three damage categories. Significant yield reduction was detected 4 wk after severe fruit damage was observed in the high and medium thrips density treatments in 1996 and 7 wk in 1998. Percentage of severe damaged fruit (P(F3)) has significant linear relationships with the adult thrips density (x) that was sampled by sticky traps 1 wk before harvest (P(F3) = -0.2533 + 0.0828x) and that was sampled by flower counts 2 wk before harvest (P(F3) = -0.2025 + 0.5490x). Based on the regression equations, economic injury levels, expressed as adult thrips per sticky trap per day or adult thrips per flower, were calculated for various combinations of control costs, yield potential and fruit prices. The economic injury levels for F. occidentalis ranged from 20 to 50 adults per sticky trap per day or 3 to 7.5 per flower as determined under average greenhouse production conditions in Ontario, Canada.     

Combining ability analysis over F1-F5 generations in diallel crosses of bread wheat

Summary Combining ability studies for grain yield and its primary component traits in diallel crosses involving seven diverse wheat cultivars of bread wheat (Triticum aestivum L.) over generations F₁-F₅ are reported. The general and specific combining ability variances were significant in all generations for all the traits except specific combining ability variance for number of spikes per plant in the F₅. The ratio of general to specific combining ability variances was significant for all the traits except grain yield in all the generations. This indicated an equal role of additive and non-additive gene effects in the inheritance of grain yield, and the predominance of the former for its component traits. The presence of significant specific combining ability variances in even the advanced generations may be the result of an additive x additive type of epistasis or evolutionary divergence among progenies in the same parental array. The relative breeding values of the parental varieties, as indicated by their general combining ability effects, did not vary much over the generations. The cheap and reliable procedure observed for making the choice of parents, selecting hybrids and predicting advanced generation (F₅) bulk hybrid performance was the determination of breeding values of the parents on the relative performance of their F₂ progeny bulks.     

A mixed model QTL analysis for sugarcane multiple-harvest-location trial data

Sugarcane-breeding programs take at least 12 years to develop new commercial cultivars. Molecular markers offer a possibility to study the genetic architecture of quantitative traits in sugarcane, and they may be used in marker-assisted selection to speed up artificial selection. Although the performance of sugarcane progenies in breeding programs are commonly evaluated across a range of locations and harvest years, many of the QTL detection methods ignore two- and three-way interactions between QTL, harvest, and location. In this work, a strategy for QTL detection in multi-harvest-location trial data, based on interval mapping and mixed models, is proposed and applied to map QTL effects on a segregating progeny from a biparental cross of pre-commercial Brazilian cultivars, evaluated at two locations and three consecutive harvest years for cane yield (tonnes per hectare), sugar yield (tonnes per hectare), fiber percent, and sucrose content. In the mixed model, we have included appropriate (co)variance structures for modeling heterogeneity and correlation of genetic effects and non-genetic residual effects. Forty-six QTLs were found: 13 QTLs for cane yield, 14 for sugar yield, 11 for fiber percent, and 8 for sucrose content. In addition, QTL by harvest, QTL by location, and QTL by harvest by location interaction effects were significant for all evaluated traits (30 QTLs showed some interaction, and 16 none). Our results contribute to a better understanding of the genetic architecture of complex traits related to biomass production and sucrose content in sugarcane.     

Association Mapping for Epistasis and Environmental Interaction of Yield Traits in 323 Cotton Cultivars under 9 Different Environments

Improving yield is a major objective for cotton breeding schemes, and lint yield and its three component traits (boll number, boll weight and lint percentage) are complex traits controlled by multiple genes and various environments. Association mapping was performed to detect markers associated with these four traits using 651 simple sequence repeats (SSRs). A mixed linear model including epistasis and environmental interaction was used to screen the loci associated with these four yield traits by 323 accessions of Gossypium hirsutum L. evaluated in nine different environments. 251 significant loci were detected to be associated with lint yield and its three components, including 69 loci with individual effects and all involved in epistasis interactions. These significant loci explain ∼ 62.05% of the phenotypic variance (ranging from 49.06% ∼ 72.29% for these four traits). It was indicated by high contribution of environmental interaction to the phenotypic variance for lint yield and boll numbers, that genetic effects of SSR loci were susceptible to environment factors. Shared loci were also observed among these four traits, which may be used for simultaneous improvement in cotton breeding for yield traits. Furthermore, consistent and elite loci were screened with −Log₁₀ (P-value) >8.0 based on predicted effects of loci detected in different environments. There was one locus and 6 pairs of epistasis for lint yield, 4 loci and 10 epistasis for boll number, 15 loci and 2 epistasis for boll weight, and 2 loci and 5 epistasis for lint percentage, respectively. These results provided insights into the genetic basis of lint yield and its components and may be useful for marker-assisted breeding to improve cotton production.     

籼型光敏核不育水稻育性可转换性的基因定位和基因互作研究

本研究以来源于农垦58S的灿型光敏核不育系培矮64S（短日条件下育性难转换）和8902S（短日条件下育性蝗转换）及其F1,F2群体为材料,通过短日不同光温和不同生态条件4种处理,利用RFLP分子标记研究了影响光敏偿育水稻在短日条件下的育性可转换性的遗传,基因定位和基因互作,主要结果表明：影响光敏不育水稻的育性可转换性表现为微效基因的作用,定位了7个控制光敏核不育水稻的育性可转换性QTL,即S2,S3a,S3b,S5,S8和S10,揭示了基因互作真实存在于光敏核不育水稻中,基因互作形式和互作类型对光敏核不育水稻的育性可转换性的影响表现多种多样,不同类型的基因互作所解释的遗传变异处于2．15％－10．07％之间。     

籼型光敏核不育水稻育性可转换性的基因定位和基因互作研究

本研究以来源于农垦58S的籼型光敏核不育系培矮64S(短日条件下育性难转换)和8902S(短日条件下育性易转换)及其F１、F２群体为材料,通过短日不同光温和不同生态条件4种处理,利用RFLP分子标记研究了影响光敏核不育水稻在短日条件下的育性可转换性的遗传、基因定位和基因互作,主要结果表明：影响光敏核不育水稻的育性可转换性表现为微效基因的作用,定位了7个控制光敏核不育水稻的育性可转换性QTL,即S2、S3a、S3b、S5、S8和S10。揭示了基因互作真实存在于光敏核不育水稻中,基因互作形式和互作类型对光敏核不育水稻的育性可转换性的影响表现多种多样,不同类型的基因互作所解释的遗传变异处于2.15%～10.07%之间。     

QTL Analysis for Root Protein in a Backcross Family of Cassava Derived from Manihot esculenta ssp flabellifolia

Root protein content of elite cassava is very low, largely due to breeder’s selection for other agronomic traits mainly fresh weight yield and disease resistance. Increased protein content in the root of cassava will improve its usefulness as a more complete food source in the developing world. An inter-specific F₁ hybrid CW 198 - 11 was earlier developed at International Center for Tropical Agriculture (CIAT), Cali, Colombia by genetic crosses of OW 230 - 1 (FLA 441 - 5) and CW 30–65 (an inter-specific hybrid between an improved cassava variety SG 427 - 87 and an accession of Manihot esculenta ssp flabellifolia (MESCFLAX – 80)). The inter-specific cross was ‘backcrossed’, in the sense of another cross to cassava (MTAI – 8) to generate a B₁P₂ family with 225 progenies in which major quantitative trait loci (QTL) for root protein in the backcross population of cassava were identified. A linkage map from the female parent of the backcross population was used for QTL detection. A total of three QTL (protg.7, protg.13 and protg.23) controlling protein were identified in three different environments. One QTL was expressed across all three environments. These results demonstrated high broad sense heritability of 61.6% for protein over 2 years, in two different locations. The individual effects of alleles at these QTL explained from 15% to 25% of the phenotypic variance. The consistency of QTL controlling protein across environments reveals their potential for use in marker-assisted recurrent selection.     

Morphological markers for the detection of introgression from cultivated into wild carrot (Daucus carota L.) reveal dominant domestication traits

Hybridisation and subsequent introgression have recently received much attention in the context of genetically modified crops. But crop–wild hybrid detection in the field can be difficult, as most domestication traits seem to be recessive, and the hybrid phenotype may also depend on the direction of the cross or environmental factors. Our aim was to develop a reliable set of morphological markers that differ between two wild and 13 cultivated carrots (Daucus carota L.) and to evaluate their inheritance in hybrid lines. We then examined these morphological markers in four F1 hybrids obtained by fertilising plants from the two wild accessions with pollen from two common carrot cultivars. Of the 16 traits that differed between the two carrot subspecies, three took intermediate values in the hybrids, eight resembled the cultivar parent (dominant domestication traits), two resembled the wild parent (domestication traits recessive), and three were not significant or growth condition‐dependent. Root:shoot ratio was seven times higher for cultivars than for wild plants, while still attaining equivalent total dry weight, which shows that dry matter production by the shoot is much higher in cultivars than in wild plants. High root:shoot ratios were also present in the hybrids. While we found no maternal effects, the type of cultivar used for pollination had an impact on hybrid characteristics. The morphological markers developed here provide insights into the mode of inheritance of ecologically relevant traits and can be useful for pre‐screening wild populations for hybrid detection prior to genetic analysis.     

Phenotypic evaluation of genetic variability and selection of yield contributing traits in chickpea recombinant inbred line population under high temperature stress

Heat is a major abiotic stress that drastically reduces chickpea yield. This study aimed to identify heat-responsive traits to sustain crop productivity by screening a recombinant inbred line (RILs) population at two locations in India (Ludhiana and Faridkot). The RIL population was derived from an inter-specific cross between heat-tolerant genotype GPF 2 (C. arietinum L.) and heat sensitive accession ILWC 292 (C. reticulatum). The pooled analysis of variance showed highly significant differences for all the traits in RILs and most of the traits were significantly affected by heat stress at both locations. High values of genotypic coefficient of variation (19.52–38.53%), phenotypic coefficient of variation (20.29–39.85%), heritability (92.50–93.90%), and genetic advance as a percentage of mean (38.68–76.74%) have been observed for plant height, number of pods per plant, biomass, yield, and hundred seed weight across the heat stress environments. Association studies and principal component analysis showed a significant positive correlation of plant height, number of pods per plant, biomass, hundred seed weight, harvest index, relative leaf water content, and pollen viability with yield under both timely-sown and late-sown conditions. Path analysis revealed that biomass followed by harvest index was the major contributor to yield among the environments. Both step-wise and multiple regression analyses concluded that number of pods per plant, biomass and harvest index consistently showed high level of contribution to the total variation in yield under both timely-sown and late-sown conditions. Thus, the holistic approach of these analyses illustrated that the promising traits provide a framework for developing heat-tolerant cultivars in chickpea.Supplementary InformationThe online version contains supplementary material available at 10.1007/s12298-021-00977-5.     

温室番茄干物质分配与产量的模拟分析

根据试验资料及温室番茄(Lycopersicon esculentum)作物的生长特性,构建了基于分配指数(Partitioning index,PI)和收获指数(Harvest index,HI)与辐热积(Product of thermal effectiveness and PAR,TEP)关系的番茄干物质分配和产量预测的数学模型,并利用不同品种、基质和地点的试验资料对模型进行检验.模型对番茄地上部分干重、根系干重、茎干重、叶片干重和果干重的预测结果与1∶1直线之间的决定系数(Coefficient of determination,R²)分别为0.95、0.57、0.82、0.79和0.93;统计回归标准误差(Root mean squared error,RMSE)分别为647.0、78.1、279.0、496.9和381.8 kg·hm^-2;对产量的预测结果与1∶1直线之间的R²和RMSE分别为0.88和5 828.5 kg·hm^-2;不仅预测精度较高,且参数少、用户易于获取,为温室番茄模型应用于温室番茄生产的优化管理奠定了基础.     

Root traits and taxonomic affiliation of nine herbaceous species grown in glasshouse conditions

This study examines whether root traits differed between three major plant families (Asteraceae, Fabaceae and Poaceae) and whether they are related to root respiration and exudation. Nine traits related to biomass allocation, root topology, morphology, chemical composition and mycorrhizal colonisation were examined for nine C₃ herbaceous species grown in controlled conditions. Poaceae differed from Fabaceae for the whole set of root traits examined except mycorrhizal colonisation, while Asteraceae showed intermediate characteristics. As compared to Fabaceae, Poaceae allocated more biomass to roots; showed a more sparsely branched root system with a small average root diameter, a high root dry matter content and a low nitrogen concentration. Root respiration was weakly related to root mass ratio and root dry matter content; no significant relationship was found between root functions and root architecture or morphology. This study shows that plant classification based on taxonomic affiliation reflects differences in root system traits and functions. Whole root system traits do not allow strong predictions of root respiration and exudation, perhaps because these processes are more linked to fine root than to whole root system traits.     

Triple test cross analysis in F2 populations of four barley crosses

Summary The triple test cross analysis of Jinks and Perkins (1970) was used to study different components of genetic variation in four barley F₂ populations, C 164x IB 226, C 164xJyoti, IB 226xP 113 and DL 3xP 113, for final plant height, spike length, 100-kernel weight, grain yield per plant and harvest index. The overall epistasis (i type) was, in general, a minor component but the j & 1 type epistasis was an important element for all five characters in cross 3 (IB 226xP 113). Both the additive (D) and dominance (H) components were highly significant for all the five characters in all four crosses. The dominance was directional in all cases except for 100-grain weight in crosses 1 (C 164xIB 226), 2 (C 164xJyoti) and 4(DL 3xP 113).