Use of component analysis in QTL mapping of complex crop traits: a case study on yield in barley

Genes contributing to the quantitative variation of a complex crop trait can be numerous. However, using existing approaches, the number of quantitative trait loci (QTL) detected for a trait is limited. Therefore, rather than looking for QTL for a complex trait itself, determining QTL for underlying component traits might give more information. In this study the potential of component analysis in QTL mapping of complex traits was examined using grain yield in spring barley as an example. Grain yield was divided into three components: number of spikes/m², number of kernels/spike, and 1000‐kernel weight. These traits were measured for individuals of a recombinant inbred‐line population in field trials conducted over 2 years. By the use of an approximate multiple QTL model, one to eight QTL were detected for each trait in a year. Some QTL were mapped to similar positions in both years. Almost all QTL for yield were found at the position of or in close proximity to QTL for its component traits. A number of QTL for component traits were not detected when yield itself was subjected to QTL analysis. However, relative to the QTL for yield itself, all component‐trait QTL did not explain the variation in yield better. The results in relation to the potential of using component analysis in studying complex crop traits are discussed.     

Genetic diversity and relationships among pea cultivars revealed by RAPDs and AFLPs

In order to obtain an overview of the genetic diversity present within the set of pea cultivars released in Germany, 21 cultivars were analysed at the DNA level by random amplified polymorphic DNAs (RAPDs) and amplified fragment length polymorphisms (AFLPs), as well as for agronomic traits. Yield of grain cultivars ranged from 2.95 to 3.87 t/ha. Based on the screening of 60 RAPD primers and 32 Eco RI + 3/Mse I+3 AFLP primer combinations, 20 RAPD primers and 11 Eco RI + 3/MseI+ 3 primer combinations generating polymorphic and distinct fragments were chosen for estimation of genetic diversity. Twenty RAPD primers amplified a total of 314 scorable bands ranging from about 262 bp to 1996 bp. Of these, 175 fragments (55.7%) were polymorphic. Based on these data, genetic similarity (GS) was estimated between 0.80 (‘Lisa’ vs.‘Grapis’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’; mean GS = 0.88). Eleven AFLP primer combinations led to the amplification of 949 scorable fragments ranging from 43 to 805 bp and of these, 462 (48.7%) were polymorphic. Genetic similarity based on AFLPs was calculated between 0.85 (‘Lisa’ vs.‘Laser’) and 0.94 (‘Bohatyr’ vs. ‘Sponsor’, mean GS = 0.90). Correlation of genetic similarity estimated on RAPDs and AFLPs was estimated at r = 0.79** using Spearman's rank correlation coefficient and at r = 0.84 by the Mantel test, respectively. UPGMA cluster analysis carried out on these data separately for RAPDs and AFLPs and on the combined data reflected, to some extent, pedigree relationships and cophenetic correlations (r = 0.89 for RAPDs, r = 0.88 for AFLPs, and r = 0.93 RAPDs + AFLPs) indicate a good fit of respective clusters to genetic similarity data. The correlation of cluster analyses to pedigree information and the impact on parental genotype selection is discussed.     

Mapping QTLs for Yield Stability in Durum Wheat Grown under Different Water Regimes

Among the most important Mediterranean annual crops, durum wheat is widely grown in drought-prone areas. Therefore, improving water-use efficiency （WUE） of durum wheat represents a major breeding goal. IDu-WUE （Improving Durum wheat for Water Use Efficiency and yield stability through physiological and molecular approaches） is a collaborative project among public and private research centres in Italy, Spain and WANA （West Asia and North Africa） countries （Morocco, Tunisia, Syria and Lebanon） funded by the European Union aimed at investigating the genetic variation for WUE and yield stability in durum wheat grown in Mediterranean droughtprone areas. During the first year of the project, a number of morpho-physiological traits （e.g. early vigour, flowering time, leaf rolling, number of fertile tillers, etc.）, WUE, WUE-related traits （e.g. carbon isotope discrimination, canopy temperature, chlorophyll fluorescence, etc.）, yield and its components have been investigated in a RIL population （249 lines） and a collection of ca. 190 durum wheat accessions characterized by a high level of linkage disequilibrium （Maccaferri et al., 2005）,     

An Effect of Various Nitrogen Forms Used as Fertilizer on Lupinus albus L. Yield and Protein, Alkaloid and α-Galactosides Content

The influence of various forms of nitrogen supplied to the ground as N₂, NH, NO, [NH + NO], –NH₂, and Nd (N‐deficiency) on Lupinus albus L. cvs. Butan (sweet) and Bac (bitter) yield and protein, alkaloid and α‐galactoside biosynthesis in their seeds were studied. The experiments were performed in a greenhouse on perlite using, in all cases, the same dose of P, K, Mg and micronutrients (B, Zn, Mn, Cu, Mo, Fe). The Nd treatment contained only macro‐ and micronutrients without any nitrogen support. We found that different nitrogen forms used as a fertilizer had a significant influence on the development and yield structure of both lupin cultivars. It was found that the plants developed most favourably when nitrogen was supplied as N₂ and [NH + NO]. For the other forms, the anomalies like necrosis, chlorosis, leaves with small surface of assimilation were noticed. However, these observations were not always reflected by all parameters of yield structure. The forms of nitrogen had a pivotal influence on yield of generative and vegetative parts of lupin. Moreover, significant differences in protein, alkaloid and α‐galactoside content in seeds were observed.     

Nitrogen Accumulation and Translocation for Winter Wheat under Different Irrigation Regimes

The translocation of pre‐anthesis nitrogen to the grain is an important source for winter wheat. The relation between the nitrogen translocation and irrigation regime was studied in the field under a rain‐proof trough shelter. Nitrogen (N) translocation amount, N translocation efficiency decreased with a decline in irrigation amount or by excessive irrigation. Compared with different organs, the leaf and stem had higher N translocation amounts, and contributions to grain for both cultivars – Jinan 17 and Lumai 21, indicating that stem also is a major N source for grain development. The contribution of pre‐anthesis total above ground N to grain N ranged from 57 to 76 %, indicating the importance of pre‐anthesis storage of N for achieving high grain N concentrations. Grain nitrogen and yield (kg ha^?1) were positively and significantly correlated with the N translocation amounts and contributions, respectively, suggesting that the sink strength may be involved in the translocation of N from a vegetative organ to the grain. N harvest index (NHI) was significantly correlated with N translocation efficiency, suggesting that the latter is a prerequisite for increasing grain N and improving grain quality. The experiment showed that N translocation status is enhanced by better irrigation practices, but limited by severely deficient or excessive irrigation.     

Characterization ofSolanum tuberosum simple sequence repeats and application to potato culiwar identification

With the continued introduction of new potato cultivars, accurate identification is becoming difficult but is essential for maintaining cultivar integrity and Plant Breeders’ Rights. Hypervariable DNA sequences, referred to as simple sequence repeats (SSRs) or microsatellites, have been reported to be an excellent source of genetic markers. To determine the abundance, distribution, and composition of SSRs withinSolanium tuberosum, 252 sequences were searched for tetranucleotide and smaller SSRs with a minimum length of 20 nucleotides and a maximum discrepancy of two nucleotides. In total, 40 unique SSRs were observed in the 252S. tuberosum sequences examined and occurred at a frequency of one SSR every 8.1 kb. To assess the ability of site-specific amplified SSRs to identify potato cultivars, a simple (TCAC)_m and compound (TCAC)_m ? (CTT)_n SSR 5’ to the starch synthase gene and a compound (C)_p ? (CT)_q ? (AT)_r ? (G)_s SSR 5’ to the sequence encoding mature proteinase inhibitor I, were examined and shown to produce unique DNA profiles for 73 of 95 tetraploid cultivars. In total, 24 alleles were observed at these loci and the accurately sized amplified DNA products can be used to establish a database for cultivar identification. Site-specific amplified alleles were somatically stable and have been conserved in clonal variants of Russet Burbank independently maintained for almost seven decades, a characteristic essential for cultivar identification. As genetic markers, the abundant, informative, and easily examined site-specific amplified alleles of SSRs are ideal for quickly and accurately determining cultivar identity of S.tuberosum ssp.tuberosum.     

Phenotypic stability of resistance to late blight in potato clones evaluated at eight sites in the United States

Changes in the fungal pathogenPhytophthora infestans in the United States pose a significant threat to potato production. Sources of resistance to these new genotypes of P.infestans need to be identified for potato breeders to have parental materials for crossing, and the phenotypic stability of late blight resistance in these potato clones needs to be determined. Sixteen potato clones which reportedly have some resistance to late blight were evaluated at eight locations: Florida (FL), Maine (ME), Michigan (MI), Minnesota (MN), North Dakota (ND), New York (NY), Pennsylvania (PA) and Wisconsin (WI) in 1996. Percent infected foliage was recorded at approximately weekly intervals following the onset of the disease at each location. Area under the disease progress curve (AUDPC) was calculated. Clones were ranked for mean AUDPC within location and the nonparametric stability statistics, mean absolute rank differences and variance of the ranks, were analyzed for phenotypic stability. Neither of these statistics was significant, indicating a lack of genotype x environment interaction on the rankings of these clones across locations in 1996. The four clones with lowest AUDPC scores were U.S. clones AWN86514-2, B0692-4, B0718-3 and B0767-2. These clones should be useful parental materials for breeders seeking to incorporate genes for late blight resistance into potatoes.     

Potato production and incidence ofVerticillium dahliae following rotation to nonhost crops and soil fumigation in the state of Washington

For three years, potato yields, tuber quality, and incidence ofVerticillium dahliae were measured in field plots previously cropped for one year to the following nonhosts: sudan grass, green peas followed by sudan grass (same year), spring wheat, spring wheat followed by sudan grass (same year), sweet corn and field corn. One year rotation to nonhosts did not reduce the population ofV. dahliae propagules in the soil and in only one of the three years wereV. dahliae propagule numbers in potato stems significantly reduced in plots following nonhost crops, compared with plots following potatoes. Verticillium wilt symptoms in potatoes were not reduced by one year rotation to any of these crops and only in one year in three was yield significantly increased. In two of three years, percent U.S. No. 1 tubers was increased following one-year rotation with green peas plus sudan grass, and in one of the two years, specific gravity was increased by rotation. Rotational cropping to nonhosts for two years between potatoes significantly reduced preplant soil populations ofV. dahliae propagules in the soil and in potato stems the following fall. However, soil populations in these two year rotational plots the spring following potato were not reduced compared to plots previously cropped to potatoes two consecutive years. Cropping to nonhosts for two years had no consistent effect on incidence of Verticillium wilt in subsequent potato crops. Two years’ rotation to nonhosts increased plant height and yield compared to continuous cropping to potato but not percent U.S. No. 1 tubers. The various nonhost crops all had about the same non-significant effect on yield. In two out of three years’ trials, fumigation significantly reduced both the incidence of Verticillium wilt and number ofV. dahliae propagules in stems in plots compared to plots non-fumigated. In only one trial, fumigation significantly increased tuber yields and percent U.S. No. 1 tubers.     

The productivity of four forage legumes sown alone and with each of five companion grasses

Four legumes—white clover cv. Blanca, red clover cvs Violetta (diploid) and Hungaropoly (tetraploid) and lucerne cv. Europe—were established as pure-sown swards and with each of five companion grasses: timothy cv. Timo, meadow fescue cv. Bundy, sweet brome cv. Deborah and perennial ryegrass cvs Talbot (diploid) and Barlatra (tetraploid), both ryegrasses being of 'intermediate' heading date. Two 'silage' crops and an 'aftermath grazing' crop were harvested in each of three successive years.
In the first harvest year, total herbage DM production of red clover ranged from 15·03 to 17·01 t ha^-1. White clover and lucerne swards produced considerably less at 7·12 to 11·01 t ha^-1. In the second harvest year, lucerne swards were the highest producing at 15·54 to 17·14 t ha^-1, while DM production from red clover and white clover swards ranged from 6·75 to 11·87 t ha^-1. Lucerne swards maintained their production superiority in the third year at 16·48 to 17·87 t ha^-1, while production from white clover swards ranged from 6·41 to 10·23 t ha^-1. However, red clover swards declined to 3·30 to 5·81 t ha ^-1; this above-average decline was mainly caused by the onset of red clover necrotic mosaic virus which affected all red clover plots uniformly in the second harvest year, and by winter conditions before the third harvest year. Total herbage DOM and CP yields of the swards were influenced in a similar manner to DM production.     

The potential of an all-grass diet for the late-winter calving dairy cow

In a trial lasting 3 years at Jealott's Hill and 2 years at Ravenscroft Hall, a total of 73 January- March-calving Friesian x Holstein cows and heifers were given a diet consisting almost exclusively of ensiled and grazed ryegrass for an entire lactation to establish the level of milk production which grass alone can support. From calving to turnout in April/May (average duration 87 days), the animals were given high digestibility (DOMD = 678g kg-¹ DM) ryegrass silage ad libitum. After turnout, they grazed ryegrass swards until housing in autumn. Thereafter, the cattle were given ryegrass silage of lower digestibility (DOMD = 600–620 g kg-¹ DM) for the remainder of the lactation and during the dry period.
Mean silage dry matter intakes from calving to turnout were 13–2 kg day-¹ at Jealott's Hill and 11·5 kg day-¹ at Ravenscroft Hall. Average milk yields were 21-1 kg day-¹ for cows and 16-1 kg day-¹ for heifers with 39-2g fat kg-¹, 29-6g protein kg-¹ and 47–9 g lactose kg-¹. Over the complete lactation, average milk yields were 4680 kg and 4006 kg for the cows and heifers, respectively, with 39-4 g fat kg-¹, 31·4 g protein kg-¹ and 46·9 g lactose kg-¹. Animal health and fertility were satisfactory. The results demonstrated the value of high quality grazed and ensiled ryegrass and provided a measure of milk production from grass only.