Methods to predict transgressive segregation in barley and other self-pollinated crops

Most of agronomically important characters are biometric traits. An improvement of these traits in cultivated plants by deriving segregants superior to parents, which could be developed as cultivars, is a main goal in breeding of self-pollinated crops. Two problems need to be solved: when will the progeny be better than its parents and how can a genetic potential of a given pair of parental genotypes be predicted? In this paper, transgressive segregation in homozygous barley populations is shortly reviewed. Various approaches to choosing parental forms are shown, and a theoretical method for predicting the frequency of transgressive segregants in a homozygous population is presented. Additionally, relationships between parental diversity estimated with molecular markers and the progeny performance are discussed. Although the prediction of transgressive segregation is still a problem, it seems promising to apply an approach measuring the performance of the parental genotypes and estimating their genetic distance by molecular markers.     

Leaf senescence and N uptake parameters as selection traits for nitrogen efficiency of oilseed rape cultivars

The cultivation of N-efficient oilseed rape cultivars could contribute to a reduction of the large N balance surpluses of this crop. To facilitate the breeding process of N-efficient cultivars, the identification of secondary plant traits correlating with N efficiency is necessary. The objectives of this study were to investigate leaf senescence and N uptake parameters of oilseed rape cultivars and doubled haploid (DH) lines with contrasting N efficiency in a short-term nutrient solution experiment and to relate these results to their performance in field experiments. In the nutrient solution experiment, genotypes differed in leaf senescence of fully expanded leaves and maximum N uptake rate per unit root length under low N supply. A high maximum N uptake rate seemed to have contributed to delayed leaf senescence by enhancing N accumulation in leaves. Also in the field experiments, genotypes differed in leaf senescence after flowering at limiting N supply. Additionally, the most N-efficient DH line was able to adapt leaf photosynthetic capacity to the low-light conditions in the canopy during flowering. N efficiency (grain yield at limiting N supply) was positively correlated with delayed leaf senescence both in nutrient solution and field experiments. It is concluded that important leaf and root traits of N-efficient cultivars are expressed in short-term nutrient solution experiments, which may facilitate the selection of N-efficient cultivars.     

Evaluation of the best linear unbiased prediction method for breeding values of fruit-quality traits in citrus

Fruit-quality trait improvement is an important objective in citrus breeding; however, fruit breeding programs often accumulate highly unbalanced phenotypic records, which are a serious obstacle in comparing and selecting genotypes. The best linear unbiased prediction (BLUP) method can be used to overcome these difficulties, but few fruit breeding programs have adopted the method, and to our knowledge, the method has not yet been used to predict breeding values of traits based on pedigree information and genetic correlations between traits in citrus. Accordingly, we used the BLUP method to predict the breeding values of nine fruit-quality traits (fruit weight, fruit skin color, fruit surface texture, peelability, flesh color, pulp firmness, segment firmness, sugar content, and acid content) utilizing phenotypic records collected over several years as part of the citrus breeding program conducted at the Kuchinotsu branch of the National Institute of Fruit Tree Science in Japan. Although the accumulated phenotypic records were highly unbalanced, the BLUP method was able to predict the breeding values of all 2122 genotypes (111 parental cultivars and 2011 F₁ offspring from 126 pair-cross families), as well as estimates of several genetic parameters, including narrow-sense heritability and phenotypic and genotypic correlations. These findings demonstrate the utility of the BLUP method in citrus crossbreeding and provide predicted breeding values, which can be used to select superior genotypes in the Kuchinotsu Citrus Breeding Program and related genetic selection endeavors.     

Variation in Cell Wall Composition and Accessibility in Relation to Biofuel Potential of Short Rotation Coppice Willows

Short rotation coppice (SRC) willow is currently emerging as an important dedicated lignocellulosic energy crop in the UK. However, investigation into the variation between species and genotypes in their suitability for liquid transport biofuel processing has been limited. To address this, four traits relevant to biofuel processing (composition, enzymatic saccharification, response to pretreatment and projected ethanol yields) were studied in 35 genotypes of willow including Europe’s leading SRC willow cultivars. Large, genotype-specific variation was observed for all four traits. Significant positive correlations were identified between the accessibility of glucan to enzymatic saccharification before and after pretreatment as well as glucose release and xylose release via acid hydrolysis during pretreatment. Of particular interest is that the lignin content of the biomass did not correlate with accessibility of glucan to enzymatic saccharification. The genotype-specific variations identified have implications for SRC willow breeding and for potential reductions in both the net energy expenditure and environmental impact of the lignocellulosic biofuel process chain. The large range of projected ethanol yields demonstrate the importance of feedstock selection based on an ideotype encompassing the performance of both field biomass growth and ease of conversion.     

Genetic diversity changes in Indian lentils over the times

The genetic diversity of 96 genotypes of lentil comprising 34 cultivars, 46 advanced breeding lines, and 16 germplasm lines were studied using 260 SSR markers. These markers generated a total of 749 alleles. The alleles/locus ranged from 2 to 16 with an average value of 2.87. Polymorphic information content varied from 0.02 to 0.91 with a mean of 0.30. Major allelic frequency ranged from 0.14 to 0.99 with a mean of 0.77. Studied genotypes were clustered into two groups according to their breeding history. Advanced breeding lines derived from exotic lines were clustered in one group, while another group accommodated most of the cultivars and advanced breeding lines with common cultivars in parentage. The germplasm lines were sub-clustered within first group. Cumulatively, first three principal components contributed 21.2% to the total variability. Advanced breeding lines showed higher number of alleles/locus and gene diversity (He) than other sets of genetic materials. In present study, no significant differences were observed between cultivars developed in different decadal groups for both NA and He. Moreover, genetic diversity changes between small and large seeded lentil cultivars were also found non-significant in this study. These findings showed that the use of alien genes can help to diversify active gene pool for developing improved new cultivars in lentil.     

Genetic Diversity of Iranian Accessions,Improved Lines of Chickpea (<Emphasis Type="Italic">Cicer arietinum L.</Emphasis>) and Their Wild Relatives by Using Simple Sequence Repeats

Biodiversity information in available germplasm is very useful for the success of any breeding program. To establish genetic diversity among 44 genotypes of chickpea comprising cultigen, landraces, internationally developed improved lines and wild relatives, genetic distances were evaluated using 19 simple sequence repeat markers with 100 marker loci. Estimation of the number of alleles per locus (n _a), the effective allele number (n _e), and Wright fixation index F were 6.25, 3.67, and 0.44, respectively. Polymorphism information content values ranged from 0.84 (locus NCPGR6 and TA135) to 0.44 (locus NCPGR7) with an average of 0.68. Dice’s coefficient similarity matrix for studied chickpea genotypes varied from 0.07 to 1.0 indicating a broader genetic base among genotypes studied. The highest similarity, 1.0, was observed between genotypes Sel 96TH11484 and Sel 96TH11485; while, the lowest, 0.07, was observed between genotypes Sel 95TH1716 and Azad. Based on the UPGMA clustering method, all genotypes were clustered in eight groups, which indicated the probable origin and region similarity of landraces and local Iran landraces over the other cultivars and wild species. It also represents a wide diversity among available germplasm. Analysis of molecular variance revealed that 41% of the total variance was due to differences among groups while 59% was due to differences within groups. The results of principal coordinate analysis approximately corresponded to those obtained through cluster analysis. Genetic variation detected in this study can be useful for selective breeding for specific traits and in enhancing the genetic base of breeding programs.     

Genetic diversity among alfalfa (Medicago sativa) cultivars coming from a breeding program, using SSR markers

Alfalfa (Medicago sativa) is an autotetraploid, allogamous and heterozygous species whose cultivars are synthetic populations. The breeders apply selection pressure for some agronomic traits within a breeding pool to increase the frequency of favorable individuals. The objective of this study was to investigate the differentiation level among seven cultivars originating from one breeding program, and between these cultivars and the breeding pool, with eight SSR markers. These highly polymorphic and codominant markers, together with recent population genetic statistics extended to autotetraploids, offer tools to analyse genetic diversity in alfalfa. The number of alleles per locus varied between 3 and 24. All loci were at a panmictic equilibrium in the cultivars, except one, probably because of null alleles. With seven SSR loci, each cultivar was at panmictic equilibrium. The mean gene diversity was high, ranging from 0.665 to 0.717 in the cultivars. The parameter F _ST indicated a low but significant diversity among cultivars. Among 21 pairs of cultivars, 15 were significantly different. The breeding pool also had a high diversity, and was significantly different from each cultivar except the most recent one. Considering the characteristics of the breeding program and the mode of cultivar elaboration, we found that they were unable to generate a large variety differentiation. Estimation of population genetics parameters at SSR loci can be applied for assessing the differences between cultivars or populations, either for variety distinction or the management of genetic resources.     

Screening of rice (Oryza sativa L.) genotypes for physiological characters contributing to salinity resistance,and their relationship to overall performance

Summary Phenotypic resistance of salinity is expressed as the ability to survive and grow in a salinised medium. Some subjective measure of overall performance has normally been used in plant breeding programmes aimed at increasing salinity resistance, not only to evaluate progeny, but to select parents. Salinity resistance has, at least implicitly, been treated as a single trait. Physiological studies of rice suggest that a range of characteristics (such as low shoot sodium concentration, compartmentation of salt in older rather than younger leaves, tolerance to salt within leaves and plant vigour) would increase the ability of the plant to cope with salinity. We describe the screening of a large number of rice genotypes for overall performance (using an objective measure based on survival) and for the aforementioned physiological traits. There was wide variation in all the characters studied, but only vigour was strongly correlated with survival. Shoot sodium concentration, which a priori is expected to be important, accounted for only a small proportion of the variability in the survival of salinity. Tissue tolerance (the cellular component of resistance reflecting the ability to compartmentalise salt within leaves) revealed a fivefold range between genotypes in the tolerance of their leaves to salt, but this was not correlated positively with survival. On the basis of such (lack of) correlation, these traits would be rejected in normal plant breeding practice, but we discuss the fallacies involved in attempting correlation between individual traits and the overall performance of a salt-sensitive species in saline conditions. We conclude that whilst overall performance (survival) can be used to evaluate the salt resistance of a genotype, it is not the basis on which parents should be selected to construct a complex character through breeding. It was the norm for varieties which had one good characteristic affecting salt resistance to be unexceptional or poor in the others. This constitutes experimental evidence that the potential for salt resistance present in the rice genome has not been realised in genotypes currently extant. The results are discussed in relation to the use of physiological traits in plant breeding, with particular reference to environmental stresses that do not affect a significant part of a species' ecological range.     

Characterization of <Emphasis Type="Italic">Brassica napus</Emphasis> L. genotypes utilizing sequence-related amplified polymorphism and genotyping by sequencing in association with cluster analysis

Identifying parental combinations that exhibit high heterosis is a constant target for commercial Brassica napus L. hybrid development programs. Finding high heterotic parental combinations can require hundreds of test crosses and years of yield evaluation. Heterotic pool development could be used to divide breeding material into specific breeding pools and focus the number of parental combinations created. Here, we report the genotypic characterization of 79 B. napus genotypes by calculating genetic distance based on sequence-related amplified polymorphism (SRAP) and genotyping by sequencing (GBS) in association with a neighbour-joining clustering algorithm. Despite the different genotypic analyses, neighbour-joining cluster analysis based on genetic distance of SRAP and GBS produced similar clusters. Homology between SRAP and GBS clusters was approximately 77 % when manually comparing clusters and 68 % when comparing clusters using Compare2Trees. This research demonstrates that SRAP can have similar efficacy when compared to next-generation sequencing technology for heterotic pool classification. This information may provide an important breeding scaffold for the development of hybrid cultivars based upon genetic distance and cluster analysis.     

Generating and maintaining diversity at the elite level in crop breeding

Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may "pollute" the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.     

Models and tools for studying drought stress responses in peas

The pea (Pisum sativum L.) is an important pulse crop but the growing area is limited because of its relatively low yield stability. In many parts of the world the most important abiotic factor limiting the survival and yield of plants is the restricted water supply, and the crop productivity can only be increased by improving drought tolerance. Development of pea cultivars well adapted to dry conditions has been one of the major tasks in breeding programs. Conventional breeding of new cultivars for dry conditions required extensive selection and testing for yield performance over diverse environments using various biometrical approaches. Several morphological and biochemical traits have been proven to be related to drought resistance, and methods based on physiological attributes can also be used in development of better varieties. Osmoregulation plays a role in the maintenance of turgor pressure under water stress conditions, and information on the behaviour of genotypes under osmotic stress can help selection for drought resistance. Biotechnological approaches including in vitro test, genetic transformation, and the use of molecular markers and mutants could be useful tools in breeding of pea. In this minireview we summarized the present status of different approaches related to drought stress improvement in the pea.     

Genetic Variability in Pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis> L.) Estimated by Morphological Data and Amplified Fragment Length Polymorphism Markers

Data on genetic similarity among crop cultivars is of vital importance for the plant breeder. The objectives of this study were to group pepper (Capsicum annuum L.) genotypes into clusters according to their distances as estimated by morphological traits and amplified fragment length polymorphism (AFLP) markers and to assess the relationships between the two. Thirty-nine pepper genotypes obtained from different countries were grown in the greenhouse at University of the Free State, South Africa, during 2001 and 2002 in a randomized complete block design with three replications. A total of 20 different morphological traits were measured and six AFLP primer pairs were used to estimate pairwise genetic distances. Both datasets showed high genetic distances among the different genotypes, indicating high genetic diversity among them. The mean genetic distance among Ethiopian pungent elongated-fruit genotypes, was lower than that between them and the introduced ones. Morphological and AFLP distance estimations generally clustered together genotypes with similar fruit sizes. Significant, positive correlation was observed between morphological and AFLP diversity estimations. The narrow genetic basis among the Ethiopian pungent elongated-fruit cultivars suggests that the pepper breeding program of Ethiopia should focus on enriching its germplasm through local collection and introductions from other parts of the world.     

Performance index: An expeditious tool to screen for improved drought resistance in the Lathyrus genus

Some species of the Lathyrus genus are among the most promising crops for marginal lands, with high resilience to drought, flood, and fungal diseases, combined with high yields and seed nutritional value. However, lack of knowledge on the mechanisms underlying its outstanding performance and methodologies to identify elite genotypes has hampered its proper use in breeding. Chlorophyll a fast fluorescence transient(JIP test), was used to evaluate water deficit(WD)resistance in Lathyrus genus. Our results reveal unaltered photochemical values for all studied genotypes showing resistance to mild WD. Under severe WD, two Lathyrus sativus genotypes showed remarkable resilience maintaining the photochemical efficiency, contrary to other genotypes studied.Performance index(PIABS) is the best parameter to screen genotypes with improved performance and grain production under WD. Moreover, we found that JIP indices are good indicators of genotypic grain production under WD. Quantum yield of electron transport(wEo) and efficiency with which trapped excitons can move electrons further than QA(c0)revealed as important traits related to improved photosynthetic performance and should be exploited in future Lathyrus germplasm improvements. The JIP test herein described showed to be an expeditious tool to screen and to identify elite genotypes with improved drought resistance.     

Bemisia tabaci (Hemiptera: Aleyrodidae) biotype B colonisation and leaf morphology relationships in upland cotton cultivars

Cultivars of upland cotton, Gossypium hirsutum L., are widely grown throughout the world for fibre production. They are also good reproductive hosts for Bemisia tabaci (Gennadius) biotype B. We studied the relationships between cotton leaf morphology and whitefly population densities in eight United States Deltapine and six Australian cotton cultivars and breeding lines at Holtville, California, in 1996. Results showed that okra-leaf cultivars and lines were colonised with fewer whitefly adults, eggs and nymphs compared to normal-leaf cultivars. The distance from underleaf surfaces of cotton leaves to the centres of nearest minor vascular bundles was negatively correlated with whitefly adult, egg and nymphal densities on leaves for all genotypes with the exception of the Australian breeding line 89013–114. Our results suggest that okra-leaf and distance from underleaf surfaces to the centre of nearest minor vascular bundles of cotton leaves are genetic traits that have potential for breeding whitefly-resistant upland cotton cultivars.     

Genetic diversity in peach [Prunus persica (L.) Batsch] at the University of Florida: past,present and future

The University of Florida (UF) stone fruit breeding and genetics program was created in 1952 to develop early ripening stone fruit cultivars with high quality, adaptation to summer rainfall, low chilling requirements, and the ability to withstand high disease pressure. Diverse germplasm sources were used to introduce desirable traits in UF breeding pool. The main objective of this research was to determine the genetic diversity and population structure of the breeding germplasm, and to search for loci under selection. A total of 195 peach genotypes were used: UF cultivars and advanced selections (n?=?168), cultivars and selections from the UF-UGA-USDA joint breeding effort (n?=?13), landrace cultivars (n?=?4), high-chilling cultivars released by NCSU (n?=?5), and related Prunus (n?=?5) species. A total of 36 SSR markers distributed across the peach genome amplified 423 alleles. An average of 18 genotypes were detected per marker: A (number of observed alleles) of 11.43, Ae (effective number of alleles) of 2.58, Ho (observed heterozygosity) of 0.4, He (expected heterozygosity) of 0.52, F (Wright’s fixation index) of 0.25, and PIC (polymorphism information content) of 0.48. UPGMA cluster analysis based on Nei’s genetic distance represented best the known pedigree information for the germplasm pools. Two major groups were observed across the germplasm corresponding to melting and non-melting flesh cultivars/selections. Population structure results supported these two major groups. Several loci closely located to genome regions where different phenotypic traits have been previously mapped were detected to be under selection.     

Genomic mating in outbred species: predicting cross usefulness with additive and total genetic covariance matrices

Diverse crops are both outbred and clonally propagated. Breeders typically use truncation selection of parents and invest significant time, land, and money evaluating the progeny of crosses to find exceptional genotypes. We developed and tested genomic mate selection criteria suitable for organisms of arbitrary homozygosity level where the full-sibling progeny are of direct interest as future parents and/or cultivars. We extended cross variance and covariance variance prediction to include dominance effects and predicted the multivariate selection index genetic variance of crosses based on haplotypes of proposed parents, marker effects, and recombination frequencies. We combined the predicted mean and variance into usefulness criteria for parent and variety development. We present an empirical study of cassava (Manihot esculenta), a staple tropical root crop. We assessed the potential to predict the multivariate genetic distribution (means, variances, and trait covariances) of 462 cassava families in terms of additive and total value using cross-validation. Most variance (89%) and covariance (70%) prediction accuracy estimates were greater than zero. The usefulness of crosses was accurately predicted with good correspondence between the predicted and the actual mean performance of family members breeders selected for advancement as new parents and candidate varieties. We also used a directional dominance model to quantify significant inbreeding depression for most traits. We predicted 47,083 possible crosses of 306 parents and contrasted them to those previously tested to show how mate selection can reveal the new potential within the germplasm. We enable breeders to consider the potential of crosses to produce future parents (progeny with top breeding values) and varieties (progeny with top own performance).     

Estimating genetic parameters of architectural and reproductive traits in young macadamia cultivars

Macadamia in the orchard environment is relatively unaltered from its natural form, and there is considerable scope to alter vegetative and reproductive architecture with the aim of improving yield efficiency through breeding. An understanding of the genetic and environmental control of architecture and the dynamics between vegetative and reproductive characteristics are fundamental to identifying traits for yield improvement. This experiment calculated the broad-sense heritability (H) of architectural traits and genetic correlations between vegetative and reproductive traits over 2 years. Cutting-grown clones (n?=?3) of 15 macadamia genotypes were subsampled from a randomised high-density plot planted in 2011 in South East Queensland, Australia, and observed for two seasons between 2015 and 2017. Clonal values from independent linear mixed models for multiple traits were combined in principal component analysis (PCA) to provide an insight to potential genetic relationships between traits, and genetic correlations were calculated from multivariate linear mixed model analysis. At the tree scale, canopy volume and yield had low H (0.07 and 0.14, respectively), implying a strong environmental influence on these complex traits. Architectural components of canopy volume and yield were considered at multiple scales, for which H ranged from 0.06 to 0.68, suggesting architectural traits at lower scales may be manipulated by breeding. Specific traits displayed strong genetic relationships with yield and canopy volume, suggesting that indirect selection for yield efficiency may be possible via selection for architectural and floral traits, to improve future macadamia cultivars.     

Genotype-environment interactions for growth and carcass traits in different pig breeds kept under conventional and organic production systems

The demand for special breeding programmes for organic pig meat production is based on the assumption that pigs kept under organic conditions need different biological properties compared with conventionally kept pigs in order to achieve a good performance. This would mean that genotype-environment interactions exist. Therefore, 682 pigs of seven different genotypes were tested for growth performance and carcass quality under conventional and organic environments at two testing stations to verify genotype-environment interactions. All genotypes achieved significantly better results within the conventional environment and there were significant interactions between genotype and environment for all the criteria of growth performance and carcass quality. The interactions are mainly caused by varying differences between organic and conventional systems within genotypes, but for all traits, except weight gain, no major shift of the ranking order within environment between genotypes. Although statistically significant genotype-environment interactions exist, the modern genotypes selected under conventional conditions are also superior to indigenous breeds under organic conditions in economically important traits. Hence, it can be concluded from these results that no special breeding programme is necessary for organic production systems.