Population structure and genetic diversity in elite sugar beet germplasm investigated with SSR markers

The assessment of genetic diversity and structuration of germplasm is essential for the efficient organization of breeding material. The objectives of the study were to (i) examine the population structure of elite sugar beet germplasm, (ii) investigate genetic diversity within and among subgroups of elite sugar beet germplasm, and (iii) assess the extent of linkage disequilibrium (LD) within elite sugar beet germplasm. A total of 111 and 178 inbred lines from the seed and pollen parent (SP and PP) heterotic gene pools, respectively, which had been genotyped with 23 SSR markers, were used in this study. Two distinct subgroups were detected within the entire germplasm set by STRUCTURE and principal coordinate analysis (PCoA). This observation was not expected because the SP heterotic pool of sugar beet was developed out of the PP heterotic pool in the late 1970s. Our observation of high LD in elite sugar beet germplasm suggests that association mapping will be possible in the examined germplasm set using a relatively low numbers of markers. However, to reduce the problem of false-positive marker-phenotype association, it might be necessary to examine the subgroups separately or apply association mapping methods which take into account this structure.     

Relationship of intra- and interpopulation tropical maize single cross hybrid performance and genetic distances computed from AFLP and SSR markers

Two sets of tropical maize inbred lines, one derived from the BR-105 population and another derived from the BR-106 population, were assayed for Amplified Fragment Length Polymorphism's (AFLP) and for Simple Sequence Repeat (SSR), in order to investigate genetic distances among lines and their relationship to heterotic group assignment and single cross yield performance. Genetic distances were on average greater for interpopulation than intrapopulation crosses for both AFLP and SSR. Cluster analysis was in agreement with the original assignment for heterotic groups. Inbred line 16, derived from BR-106, was assigned to the BR-105 set, in agreement with single cross yield performance from intra- and interpopulation crosses. However, the same pattern was not observed for SSR where another two lines from BR-106 were also assigned to the BR-105 set. Correlation coefficients of genetic distances (GD) with F₁ grain yield and heterosis were high for BR-106 ×BR-106 crosses (0.91^** and 0.82^** for AFLP and SSR, respectively), moderate for BR-105 × BR-105 crosses (0.52^* for AFLP and SSR) and low for BR-105 × BR-106 crosses (0.29 and 0.16 for AFLP and SSR, respectively). The lower correlation at interpopulation level was due to the smaller range of GD caused probably by a previous selection for combining ability. General results showed that the AFLP molecular marker is efficient in assigning maize lines to heterotic groups and that AFLP-based GD is suitable for predicting the maize single cross performance for intrapopulation crosses of broad-based populations. The efficiency of SSR in assigning lines to heterotic groups and for predicting single cross performance was smaller than AFLP. This revised version was published online in July 2006 with corrections to the Cover Date.     

Relationship between hybrid performance and genetic diversity based on RAPD markers in wheat, Triticum aestivum L.

Random amplified polymorphic DNA (RAPD) markers were generated from 20 wheat, Triticum aestivum lines. Fifty-four fragments generated by six primers of a 10-mer arbitrary sequence were used to study their potential power in differentiating parents with different characteristics and predicting the yield performance of hybrids produced from these parents. Experimental results showed that the 20 wheat lines were divided into four groups. Group I was characterized by more grains per spike, group II by heavy grains and group III by more spikes per unit area and short plants; group IV was similar to group III but had a much higher biomass yield and grain yield. Hybrids from parents in different groups were generally superior to most hybrids from parents in the same group. Both yield performance and heterosis of hybrids from parents between group I and group III were much better than those of other intergroup hybrids. These results suggest that, based on RAPD markers, it is possible to differentiate wheat lines with different performances and that the classification of parents from these markers is of predictive value for developing superior hybrids. However, genetic distance (GD) based on RAPD markers was not significantly correlated with hybrid performance and heterosis. It appears to be impossible to predict hybrid performance from GD itself.     

Relationship between hybrid performance and AFLP based genetic distance in highland maize inbred lines

The objectives of this study were to determine the crossing performance of highland maize inbred lines for grain yield, days to silk and plant height; estimate genetic distance (GD) among the inbred lines and in association with tester parents, and to investigate the relationship of GD with hybrid performance and midparent heterosis (MPH). A total of 26 inbred lines were crossed with six (population and line) testers in a factorial-mating scheme. The F_1’s and the parents were evaluated at five locations in Ethiopia. Nine amplified fragment length polymorphism (AFLP) primer pairs were used to genotype all the parents. The F_1’s were found to vary widely for grain yield and other traits measured. Yield superiority of more than 30% over the best hybrid check was obtained for some testcross hybrids. Midparent heterosis on average was moderate for grain yield and, plant height. And for days to silking, MPH values were mostly negative. Mean GD values determined from the inbred lines by population tester (0.680) and line tester (0.661) combinations were not significantly different. Cluster analysis separated the tester parents from the corresponding inbred lines. AFLP grouping of the inbred lines was in agreement with their pedigree records. Genetic distances derived from the inbred lines × all testers and from the population testers’ sub-group were not positively correlated with hybrid performance and MPH for most traits. In contrast, correlations of GDs involving the line testers’ sub-group with F_1’s and MPH were significantly positive but with low magnitude to be of predictive value.     

Relationship between genetic divergence and hybrid performance in japonica rice grown in a cold water-irrigated field

The present study was carried out to evaluate genetic divergence among eleven japonica rice cultivars and to assess the relationship between genetic distance and hybrid performance in partial non-reciprocal crosses among them. The 44 F1 hybrids along with the eleven parents were evaluated for five cold tolerance-related traits; discoloration at seedling stage, days to heading, culm length, fertility, and spikelets per panicle in a cold water screening nursery (17 ^°C). The eleven parents were examined for DNA polymorphism using amplified fragment length polymorphisms(AFLPs). A total of 855 polymorphic variants were generated and based on the polymorphism data, genetic distances (GDs) ranged from 0.023 to0.524. Very little heterosis was observed in hybrids for most of the traits,whereas heterosis was high for fertility. The correlation values of GDs with F1 performance were mostly non-significant except for discoloration and fertility. The correlations of GDs with mid-parent and better-parent heterosis were not significant and proved to be of no predictive value. Our results indicate that GDs based on AFLP markers are not useful for predicting heterosis for cold tolerance in japonica hybrids. This revised version was published online in August 2006 with corrections to the Cover Date.     

Association between AFLP-based genetic distance and hybrid performance in tropical maize

Identifying the best inbred combinations for the development of commercial hybrid maize varieties remains the main challenge to maize breeders. The aim of this work was to study associations between the genetic distance (GD) of 21 inbreds and the corresponding F₁ phenotypic data. Furthermore, the impact of grouping lines into genetically similar clusters was investigated. The 21 inbred lines were fingerprinted using amplified fragment length polymorphism markers. Parents and 210 F₁ progeny were evaluated in the field. Joint data analysis mostly revealed a tighter association between GD and the F₁ performance or mid parent heterosis in the intergroup than in the intragroup crosses. Despite these correlations, intergoup crosses should always be field‐tested before their release. Crosses showing low GD values should be discarded to avoid field‐testing costs. Better F₁ hybrid performance predictions can be achieved by integrating molecular and F₁ phenotypic data.     

绿豆SSR标记的开发及遗传多样性分析

SSR标记以其数量丰富、多态性好、共显性遗传等优点在基础研究和育种工作中发挥了重要作用,但目前绿豆基因组中的SSR标记依然较少。本研究将磁珠富集法和测序技术相结合高通量检测绿豆基因组SSR位点,鉴定出3,275,355个SSR位点,开发了2742个SSR标记。选取其中157个SSR进行PCR验证,发现有90个(57.33%)标记在10份材料中表现出多态性。挑选40个条带清晰、多态性高、染色体上均匀分布的标记对90份绿豆资源进行遗传多样性分析,单个位点检测到的等位变异数为2~8个,平均为3.0个,有效等位基因数为1.31~4.21个,平均为2.16。Nei’s基因多样性指数在0.23~0.76之间,平均为0.51。多态性信息含量为0.22~0.72,平均为0.43。聚类分析将90份材料分为2个类群,包含4个组。第I组主要由北方资源组成,第Ⅱ组种质来源较为分散,第Ⅲ组主要由山东的资源构成,第Ⅳ组包含多数河北的种质资源。本研究开发的多态性SSR标记不仅可以用于绿豆种质资源的遗传多样性分析,也将在高密度遗传图谱构建、基因定位和分子标记辅助育种中发挥重要作用。     

Relationship between genetic markers and morphological traits in a maize inbred lines collection

Summary Genetic markers (isozymes), in addition to the traits recommended by the UPOV convention, have been used in France since 1989 to characterize the maize inbred lines submitted to registration. In the years 1989. 1990 and 1991, a total of 974 inbreds has been described according to this procedure. Relationships between genetic markers were investigated and underlined the occurrence of linkage disequilibria within the tested germplasm. These disequilibria appeared to depend strongly on the breeding history of the germplasm. In some cases, these disequilibria could be related to a major progenitor (foundation effect). Relationships between genetic markers and quantitative traits were also pointed out. High coefficients of determination (up to 60%) were in some cases observed at the within group level, and also appeared to be very dependent on the major progenitors of the group of interest. The consequences of these results for breeding and distinctiveness studies are discussed.     

Evaluating genetic variation and relationships among two bromegrass species and their hybrid using RAPD and AFLP markers

The two most widely grown bromegrass species in North America are smooth bromegrass (Bromus inermis Leyss.), a hay type grass, and meadow bromegrass (Bromus riparius Rehmann), a pasture type grass. Recently a hybrid bromegrass population between the two species has been produced as a dual-purpose hay-pasture grass. Molecular markers have the potential to improve selection procedures to enhance bromegrass breeding. The objective of this study was to use RAPD and AFLP markers to determine genetic relationships and variations among bromegrass populations. Forty-three RAPD markers from 21 primers and 83 AFLP markers from seven primer combinations were used. Both marker types were able to group the individuals into their respective populations. The relationships among the individuals within each of the populations were not similar between the two marker types. Analysis of molecular variance (AMOVA) detected greater within-population variation than among-population variation for both marker types. The highest variation was observed in the hybrid population followed by meadow and then smooth bromegrass. The inter-population distance from both markers indicated that the highest genetic distance was between meadow and smooth bromegrass and lowest between smooth and hybrid bromegrass, which reflect the breeding history of the hybrid population. This study showed that both markers are capable of differentiating bromegrass genotypes into their respective populations, detecting genetic variation and relationships of the populations. Results of this study suggest that these two markers can be used in the future to enhance the current breeding practices in bromegrass, however, AFLP markers would be the marker of choice due to the high number of polymorphic markers. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of genetic diversity in cabbage cultivars using RAPD and SSR markers

Genetic relationship and diversity among seven cabbage cultivars were analyzed using RAPD and SSR markers. These cultivars are of great commercial value in India and are confirmed for their reaction to black rot caused by Xanthomonas campestris pv. campestris. However, so far the extent of genetic diversity and relatedness has not been studied in these cultivars. A total of 17 selected RAPD primers generated 90 bands, 76 of which were polymorphic (84.44%). In addition, 27 selected SSR primers generated 67 amplified bands with 59 of which were polymorphic (87.6%). Though both the marker techniques were able to discriminate the cultivars effectively, analysis of combined data of markers (RAPD and SSR) resulted in better distinction of cultivars. By combining both the markers, a total of 157 bands were detected of which 135 bands (85.98%) were polymorphic, i.e. an average of 5.95 bands per primer. High level of polymorphism (> 85%) recorded with two different marker systems indicated a high level of genetic variation existing among the cultivars. Genetic relationship estimated using similarity co-efficient (Jaccard’s) values between different pairs of cultivars varied from 0.21 to 0.77 in RAPD, 0.42 to 0.82 in SSR, and 0.43 to 0.89 with combined markers. A high correspondence had been recorded between the values of genetic variations generated by UPGMA, clustering, and scatter plot diagrams. The cultivars ‘January King Sel. Improved’ and ‘Golden Acre’ are highly divergent cultivars as demonstrated by both the marker systems.     

Mapping of rhizoctonia root rot resistance genes in sugar beet using pathogen response‐related sequences as molecular markers

Rhizoctonia root and crown rot caused by the fungus Rhizoctonia solani is a serious disease of sugar beet. An F_2:3 population from a cross between a resistant and a susceptible parent has been tested for R. solani resistance and a genetic map has been constructed from the corresponding F₂ parents. The map encompasses 38 expressed sequence tags (ESTs) with high similarity to genes which are involved in resistance reactions of plants (R‐ESTs) and 25 bacterial artificial chromosomes (BACs) containing nucleotide binding site (NBS)‐motifs typical for disease resistance genes. Three quantitative trait loci (QTL) for R. solani resistance were found on chromosomes 4, 5 and 7 collectively explaining 71% of the total phenotypic variation. A number of R‐ESTs were mapped in close distance to the R. solani resistance QTL. In contrast, the NBS‐BACs mapped to chromosomes 1, 3, 7 and 9 with two major clusters of NBS‐BACs on chromosome 3. No linkage between NBS‐BACs and R. solani resistance QTL was found. The data are discussed with regard to using R‐ESTs and NBS markers for mapping quantitative disease resistances.     

Relationship between heterosis and genetic distance based on morphological traits and AFLP markers in pepper

Genetic diversity is considered as one of the criteria for the selection of parents for hybrid breeding. The present study was undertaken to evaluate genetic divergence among seven pepper cultivars and to assess the relationship between heterosis and parental genetic distance. Twenty‐one F₁ hybrids and seven parents were evaluated for 15 morphological characters in a greenhouse and in the field. The parents were examined for DNA polymorphisms using six amplified fragment length polymorphism (AFLP) primer combinations. Cluster analysis using two genetic distance measures grouped the seven parents differently. Mid‐parent and high‐parent heterosis was observed for most characters. Most hybrids outperformed the parental lines for fruit yield, earliness and plant height. Morphological and AFLP‐based distance measurements were efficient enough to allocate pepper genotypes into heterotic groups. The correlations of morphological distances with mid‐parent heterosis were significant for days to flowering and maturity, suggesting earliness can be predicted from morphological distances of parental lines. However, the correlations of AFLP‐measured genetic distances with mid‐ and high‐parent heterosis were non‐significant for all characters, except for fruit diameter, and proved to be of no predictive value.     

Comparative assessment of genetic diversity between wild and cultivated barley using gSSR and EST‐SSR markers

Barley is an economically important cereal crop especially for feed and malt production, but its value as food is increasing due to various health benefits. Wild barley is the progenitor of modern day barley cultivars possessing a rich source of genetic variation for various biotic and abiotic stresses. Species‐specific molecular markers have great potential for efficient introgression of these important traits from wild to cultivated barley. In the present study, 140 microsatellite markers were screened to assess the genetic variation and species‐specific markers between wild and cultivated germplasm. Of these 140, a polymorphic set of 48 genomic (gSSR) and 16 EST‐SSRs amplified a total of 685 alleles. Cluster analysis discriminated all 47 accessions and classified wild and cultivated genotypes into two distinct groups, according to their geographic origin. Our analysis indicated that gSSRs were more informative than EST‐based SSRs. Results from PCoA analysis for species‐specific alleles clearly suggest that wild barley genotypes contain a higher number of unique alleles.     

Root traits and yield in sugar beet: identification of AFLP markers associated with root elongation rate

Morpho-physiological and molecular analysis were conducted to identify useful root indexes of sugar beet nutrient uptake capacity and productivity. Root architectural parameters, root elongation rate, sulfate uptake rate and glucose and fructose content in the root apex, traits involved in the plant response to sulfate stress, were evaluated in 18 sugar beet genotypes characterized by different root yield. Morpho-physiological traits, determined on 11-day-old seedlings grown in hydroponics under sulfate deprivation, showed variations from 59 to 197% and were significantly correlated (P < 0.01) with root yield. Under field conditions, the highest root yield genotype (L18), which has the highest root phenotypic values following sulfate shortage, also showed the greatest root length density and leaf relative water content, with respect to the lowest root yield genotype (L01). Bulk segregant analysis based on AFLP analysis, done on a segregating progeny obtained from the cross between the two lines L01 × L18, allowed the identification of two AFLP markers associated to the root elongation rate parameter that showed the highest variation among all the analyzed root traits. The genetic diversity of root adaptive traits and the use of marker-assisted selection aimed at increasing sugar yield under water and nutrient stress in sugar beet breeding programmes are discussed.     

Yield decrease in sugar beet caused by reduced tillage and direct drilling

In a long-term series of on-farm tillage trials (10 loessial sites in southern and eastern Germany; annual mouldboard ploughing 0.25–0.3 m deep, mulching with a rigid-tine cultivator 0.1–0.15 m deep, direct drilling with no tillage except seedbed preparation for sugar beet solely) sugar beet yield was significantly decreased by direct drilling compared to ploughing. This study was conducted to (i) show that the lower plant density caused by mulching and direct drilling contributes to yield decrease but explains effects just partially, and (ii) determine the relation between soil structural properties and sugar beet yield. In 2003–2005 plant density experiments (53,000, 65,000 and 82,000 plants ha^?1) were introduced to tillage plots on five selected environments. Yield and soil structural properties of four layers representing 0–0.43 m soil depth were determined.White sugar yield (WSY) significantly declined with direct drilling compared to ploughing treatment, whereas mulching treatment diminished WSY less pronounced. Moreover, decreasing plant density significantly lowered WSY. No interactions between tillage and plant density occurred, revealing that both factors additively affected WSY.Decreasing tillage depth increased penetration resistance (PR) and dry bulk density (DBD), and diminished air filled pore volume (AFPV) in the topsoil down to 0.27 m depth. Several soil structural parameters were closely correlated with each other as well as WSY. Variation of single parameters explained up to 60% of WSY variance attributed to tillage. Combining DBD from 0.03 to 0.07 m depth, average PR from 0.03 to 0.27 m and AFPV from 0.03 to 0.18 m soil depth explained 77% of the tillage effect. Nevertheless, multi-collinearity of soil physical parameters allowed no clear conclusions on the cause-and-effect mechanisms.Conclusively, lowered plant density and soil structure degradation due to reduced tillage may independently decrease sugar beet yield. When grown on loessial soils this crop requires mechanical loosening down to 0.15–0.20 m depth to produce high yields.     

Relationship between molecular marker heterozygosity and hybrid performance in intra- and interspecific hybrids of cotton

The present study was conducted to investigate the relationship between parental molecular marker diversity and hybrid performance in both intra‐ and interspecific hybrids of cotton to evaluate the feasibility of predicting hybrid performance using molecular markers. Three cytoplasmic male sterile (CMS) lines were crossed with 10 restorer lines to produce 22 F₁ hybrids during 2003. Of 22 F₁s, 14 hybrids were intraspecific (Gossypium hirsutum × G. hirsutum) and eight interspecific (G. hirsutum × G. barbadense). These 22 F₁ hybrids and their parents were evaluated for yield and fibre quality traits at Zhejiang University, Hangzhou, China during 2004 and 2005. Genetic distances (GD) among the parents were calculated from 56 random‐amplified polymorphic DNAs (RAPD) and 66 simple sequence repeat (SSR) marker data, and their correlation with hybrid performance and heterosis were analysed. The parents could be discriminated into G. hirsutum and G. barbadense clusters by cluster analysis based on both RAPD and SSR markers data. The correlation (r = 0.503, P ≤ 0.05) was calculated between GD_rapd (GD based on RAPD markers) and GD_ssr (GD based on SSR markers). Correlation of GD with hybrid performance and heterosis differed considerably between intra‐ and interspecific hybrids. The correlation between GD and hybrid performance was non‐significant for most of traits within the hybrids of G. hirsutum species. However, it was significantly and positively correlated for fibre length, fibre strength and elongation in interspecific hybrids. The relationship between GD and heterosis was observed to be positively significant for boll weight within hybrids of G. hirsutum with significant and negative correlations for fibre length and elongation. In conclusion, the power of predicting hybrid performance using molecular markers in cotton is low. But, the relationship between SSR marker heterozygosity and hybrid performance can be used to predict fibre length during interspecific hybrid cotton breeding.     

Relationship between molecular marker heterozygosity and hybrid performance in intra- and inter-subspecific crosses of rice

The objective of this study was to investigate the relationship between molecular marker diversity and heterosis in both intra-and inter-sub-specific hybrids of rice to evaluate the feasibility of predicting hybrid performance using molecular markers. Eleven elite lines were intermated resulting in a diallel set including 10 indica × indica, 15 japonica × japonica and 30 indica × japonica crosses. The F₁ hybrids and parents were evaluated for agronomic performance in a replicated field trial. The parental lines were tested for DNA polymorphisms with 113 restriction fragment length polymorphism (RFLP) probes covering the 12 rice chromosomes. Inter-subspecific crosses showed better performance and higher heterosis than intrasubspecific hybrids. Correlations of marker heterozygosity with hybrid performance and heterosis differed considerably between the two subspecies; they were higher in crosses within japonica subspecies than within indica subspecies. Very little correlation was detected in intersubspecific crosses. It was concluded that relationships between marker heterozygosity and hybrid performance were complex owing to germplasm diversity and the complexity of the genetic basis of heterosis. The implications of the results in predicting hybrid performance using molecular markers are discussed.     

Isozymes as genetic markers in bananas and plantains

Summary Twenty-four clones of banana and plantain representing various levels of ploidy and diploid M. balbisiana, were analysed for enzyme variants of malate dehydrogenase, phosphoglucomutase, glutamate oxaloacetate transaminase, shikimate dehydrogenase and peroxidase. Polymorphism was detected in all 5 enzyme systems. In addition, the four principal Cavendish clones, Robusta, Giant Cavendish, Dwarf Cavendish and Pisang masak hijau were found to be monomorphic for isozymes of 10 additional enzymes. Isozymes of glutamate oxaloacetate transminase were the most useful for discriminating among clones of a particular genomic group.Florida Agricultural Experiment Stations Journal Series No. 6858.     

甜菜蔗糖代谢相关酶活性与糖积累关系的研究

在甜菜不同生育时期同步测定了块根和叶片中的可溶性总糖、果糖和蔗糖含量及蔗糖代谢相关酶-酸性转化酶(AI)、中性转化酶(NI)、蔗糖合成酶(SS)和蔗糖磷酸合成酶(SPS)的活性,并对糖积累与酶活性的关系进行了分析.结果表明,甜菜蔗糖代谢的相关酶对块根的糖积累的影响要高于叶片;甜菜块根和叶片中的合成和分解酶类是协同作用进行糖积累过程,并非哪类酶在单独发挥作用;整个生育期甜菜块根的可溶性总糖、果糖和蔗糖含量均大于叶片,苗期块根中果糖是块根糖积累的主要产物,叶丛形成期块根中蔗糖是块根糖积累的主要产物.