«A. Kolodinska Brantestam Faculty of Landscape Planning, Hordiculture and Agricultural Science Department of Crop Science Alnarp Doctoral thesis ...»
Indirect comparison of QTL effects is possible by means of the current ‘Steptoe’ x ‘Morex’ map, published by Kleinhofs (2001). Ultimately, with micro-array technology and knowledge about genetics of parents, MAS should become accurate and precise. The better knowledge breeders have about genes controlling economically important traits, especially quantitatively inherited traits, the more direct crop improvement efforts can be (Clancy et al., 2003). MAS using 13 inaccurate QTL estimates still in most cases gives better results than phenotypic selection (Liu et al., 2004). Plant breeding programs should effectively use the wealth of information derived from QTL mapping studies to develop new cultivars. To date, QTL information has been used primarily in marker-assisted introgression of one or more desirable alleles into an elite background or through marker-based recurrent selection (Wingbermuehle et al., 2004). A breeder using phenotypic selection must test 1.0-16.7 times more progeny than a breeder using MAS to be assured of selecting one or more superior genotypes (Knapp, 1998).
MAS gives not only larger responses but also dramatically increases the frequencies of superior genotypes compared with phenotypic selection (Liu et al., 2004). However, the advantages of MAS over phenotypic selection are considerably reduced when conducting selection in later generations. Liu et al.
(2004) proposed a modification by combining MAS in early generations with phenotypic selection in later generations as the most efficient procedure.
The rapid development of molecular techniques and intensification of plant breeding makes it possible to change the crop faster and there is an increase in the breeding pressure on the crop. This leads to an even greater interest in questions such as: How does plant breeding affect the crop? In what way and how much has barley already changed? What changes might be expected in the future? Are there negative consequences of plant breeding and its intensification? Does breeding affect the genetic diversity of the crop? Does it pose a threat to genetic plasticity of the crop, leading to restrictions in the ability to adapt?
Genetic diversity and genetic erosion More than 30 years have passed since the scientific community raised the alarm about genetic erosion. Jack Harlan (1975) used this term in the early 1970s to describe a potentially disastrous narrowing of the germplasm base employed in improving food crops. A dramatic decrease in diversity in a cultivated crop could bring serious consequences, since genetically uniform cultivars grown over vast areas are susceptible to devastating epidemics (Baker et al., 1997). The classic example of this is the Irish potato famine of the mid 19th century or the coffee rust epidemic in Ceylon in the 1870s. More recent examples include the southern corn leaf blight epidemic in the USA in 1970 (Browning, 1988) and the mould epidemic on tobacco in the USA and Europe in the 1960s (Marshall, 1977). The variation is essential for the future breeding material, since a decrease in genetic variability in general might result in a reduction in the plasticity of the crop to respond to any environmental changes and agricultural practices (Manifesto et al., 2001). For example, climate changes in the future could bring new challenges for adaptation of the crop (Arnell, 1999).
During recent decades, extensive progress has been made in Nordic and Baltic barley breeding with respect to yield, disease resistance, etc. (Ortiz et al, 2002;
Öfversten et al., 2004), mainly due to the efficient exploitation of the genetic diversity. To ensure that this progress is maintained it is important to sustain the level of genetic diversity within the breeding material used. A reliable knowledge of the genetic diversity of the breeding material is also important in order to select parents for a new breeding cycle (Pillen et al., 2000).
14 Some studies done show evidences of a decrease in genetic diversity during the process of barley domestication (Clegg et al., 1984; Provan et al., 1999;). The replacement of landraces by modern cultivars was also an important factor contributing to genetic erosion (Hammer et al., 1996). There is a concern about a continuous decrease in genetic diversity due to the narrow genetic base of the European barley germplasm (Melchinger et al., 1994). Fishbeck (1992) mentioned
several reasons for this presumed restricted genetic base:
1. Only a few landraces from the major barley growing regions have been successfully exploited for selection of superior genotypes in the initial phase of barley breeding.
2. A small number of outstanding cultivars have been extensively used as progenitors for the development of new cultivars in recycling breeding programmes.
3. Introgression of exotic germplasm has been practised only on a limited scale.
To estimate diversity within modern cultivars using only the pedigrees is insufficient, since the breeding history does not account for the effects of selection, mutation and random genetic drift (Melchinger et al., 1994). In some cases the pedigree is not even known. Methods used to evaluate genetic variation in barley include comparison of differences in morphology, agronomic traits, isozymes and hordeins (Ortiz, 2001). Nowadays they are complemented by DNA marker analysis (Karp et al., 1997;Wolko & Kruszka, 1997; Koebner et al., 2001), which allows the observation of changes that have occurred in the cultivated barley gene pool at the genotypic level, and to compare these changes with observed phenotypic differences (Swanston & Ellis, 2002). DNA analysis shows a closer relationship for the cultivars than that estimated by the pedigree analysis, which may overestimate divergence, particularly when one parent has an ‘exotic’ genotype in its own lineage (Ellis et al., 1997).
The knowledge about marker location on chromosomes and association with gene-rich regions of barley will also give better understanding about diversity structure in the evaluated material.
To date, a number of studies have been performed to evaluate the changes in genetic diversity in barley due to plant breeding. However, these show different results depending on the country or region origin of analysed material. In some cases differences are also shown when different methods for evaluation were used.
For example, Reeves et al. (2004) in their European barley study found just a temporal flux of genetic diversity without detecting genetic erosion, similar to the results of Koebner et al. (2003) studying UK barley. Matus & Hayes (2002), on the other hand, in material from Busch agricultural Resources barley improvement programme and Russel et al. (2000) in European spring barley detected a lower diversity level within modern material.
The Nordic and Baltic region is particularly interesting for evaluation of diversity changes. One of the reasons is the specific growing conditions, mainly related to the climate, and how this has affected the material in the breeding process. The second reason is that plant breeding has been performed over a long
Objectives The general aim of this thesis was to visualise the changes in genetic diversity and relationships in Nordic and Baltic barley over the 20th century. Specific objectives
of the studies included are to:
Determine the degree of putative genetic erosion in Nordic and Baltic barley Determine the relationships between Nordic and Baltic barley Determine the genetic and phenotypic relationships between old cultivars and landraces versus modern material Detect the genetic diversity changes over time in material with different countries of origin Compare the changes in genetic diversity and relationships in two-rowed and six-rowed barley 16 Diversity in Nordic and Baltic barley Nordic (Denmark, Finland, Norway and Sweden) and Baltic (Estonia, Latvia and Lithuania) barley material representing landraces and cultivars from the end of the 19th century up to the modern cultivars and breeding lines were investigated. In this study, a number of molecular diversity evaluation methods were chosen in order to increase the reliability of the results: isozymes (paper I), ISSRs (intersimple sequence repeats) (paper II) and SSRs (simple sequence repeats) (paper III.
Study of agronomic traits was also included (paper IV). These traits represent the variation in adaptation that most probably has been affected by conscious selection. Isozymes are biochemical markers that have been successfully utilized in barley diversity studies (Linde-Laursen et al., 1987; Parzies et al., 2000). ISSRs and SSRs are DNA markers used for DNA fingerprinting and assessing genetic diversity in closely related germplasm (Röder et al., 1995; Liu et al., 1996; Martín & Sánchez-Yélamo, 2000). SSR markers are also widely used for assessing QTLs (Mesfin et al., 2003; Pillen et al., 2003).
Relationships In our study we found a distinct differentiation of two-rowed and six-rowed barley based not only on field experiments (Fig. 9), but also on the DNA analysis using ISSRs and SSRs (Fig. 10). Only the isozyme data did not demonstrate this, which was probably due to the low number of polymorphic loci.
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Fig. 9. Bi-plots of first two principal components for PCA based on the agronomical data (‘days to heading’, ‘days to maturing’, ‘plant height’, ‘harvest index’, ‘volumetric weight’ and ‘thousand kernel weight’) from a trial in Landskrona (Sweden) 2002, Symbols for accessions are ● – two-rowed landraces and cultivars before 1930; ● – two-rowed cultivars 1931-1970; ○ – two-rowed cultivars after 1971 and breeding lines; ▲ – six-rowed landraces and cultivars before 1930; ▲ – six-rowed cultivars 1931-1970; ∆ – six-rowed cultivars after 1971 and breeding lines.
17 Fig. 10. Principal coordinate analysis on ISSR (based on similarity matrix) and SSR (based on Nei 78 genetic distance matrix) data in Nordic and Baltic material.
Symbols for accessions are ● – two-rowed landraces and cultivars before 1930; ● – two-rowed cultivars 1931-1970; ○ – two-rowed cultivars after 1971 and breeding lines; ▲ – six-rowed landraces and cultivars before 1930; ▲ – six-rowed cultivars 1931-1970; ∆ – six-rowed cultivars after 1971 and breeding lines.
18 The differentiation of accessions according to the row type (Principal component analysis of agronomic data) was mainly affected by factors like ‘days to heading’, ‘days to maturing’, ‘volumetric weight’ and ‘thousand kernel weight’.
This could be expected, since the six-rowed types commonly are earlier-maturing cultivars, whereas the differences in ‘volumetric weight’ and ‘thousand kernel weight’ are associated with the spike type (Marquez-Cedillo et al., 2001). These two germplasm groups carries, according to the SSR data, also different alleles at other loci in addition to those determining lateral floret fertility. Similar results were reported by Ordon et al. (2004) in a study of German winter barley, where a clear separation and non-homogeneous allele distribution between six-rowed and two-rowed cultivars was found for most SSRs. Thus, crosses between the two germplasm groups could be expected to produce positive transgressive segregants for economically important phenotypes. However, generally two-rowed x sixrowed crosses are less successful for cultivar development (Kjær & Jensen, 1999).
This might be due to different ideotypes for two-rowed and six-rowed barley. The traits determining the ideotype are quantitative and they are distributed throughout the genome. In two-rowed cultivars there is a significant influence on yield by ‘number of ears’ but for six-rowed barley, the most significant factor is ‘number of grains per ear’ (Äyräväinen, 1976). Since the selection of these traits has been carried out probably even before commercial plant breeding started and these are quantitatively inherited traits, the difficulty in obtaining successful cultivars from direct crosses of two-rowed and six-rowed types of barley is not surprising.
The data on agronomic traits differentiated effectively the cultivars according to the breeding period (Fig. 9). The main effects on this differentiation are ‘plant height’ and ‘harvest index’. Obviously differentiation of the old and modern cultivars is due to increase in ‘harvest index’ and decrease in ‘plant height’ over time (Ortiz et al., 2002; Öfversten et al., 2004).
It was not possible to separate by molecular markers cultivars according to the breeding period in the entire data set (Fig. 10). However, the differentiation could be detected by ISSR data, and for some countries by SSR data, when gentypes from different countries were analysed separately. The differentiation between modern and old cultivars in Sweden was the most pronounced based on the SSR data (Figure 11). The variation in SSRs that accounts for differentiation between breeding periods was higher in the Swedish and Danish material than that from Finland and Norway. These differences between modern and old material in the north and south of the region might illustrate the specific objectives of the breeding programmes. In the northern part, the adaptation to the marginal growing conditions is very important and requires that locally adapted material be included in the crosses. This reliance on an adapted gene pool might explain why plant breeding in this part of the region results in fewer changes in the SSRs. The inconsistency in the marker data is probably due to the fact that different markers represent different genome regions. Most ISSRs are presumably noncoding loci dispersed throughout the genome (Wolfe & Liston, 1998), but a number of SSRs included in this study have known associations with agronomic and adaptive traits, i.e. ‘days to heading’, ‘ears per m2’, ‘grain yield’ etc. (Turpeinen et al., 2001;
Baek et al., 2003; Long et al., 2003; Pillen et al. 2003; Korff et al., 2004).
19 Fig. 11. Principal coordinate analysis on ISSR (based on similarity matrix) and SSR (based on Nei 1978 genetic distance matrix) data in material of Swedish and Norwegian origin.