Identification and validation of number of pod ‐ and seed ‐ related traits QTLs in soybean

Traits related to the number of pods and seeds are important yield factors on soybean. The relationships between phenotype and quantitative trait loci (QTLs) of these traits may reveal the mechanisms underlying productivity. Our study objectives were to analyse phenotypic correlations, detect stable QTLs and identify candidate genes useful for marker‐assisted selection. Phenotypic analyses revealed that NThSP (number of three‐seeded pods) was positively correlated with NPPP (number of pods per plant) and SNPP (number of seeds per plant). Seventy‐five QTLs were identified based on the mean phenotypic data for at least 2 years. We detected two to 15 and one to three significant QTLs identified at the same location, respectively. Six consensus QTLs associated with at least two NPS‐related (number of pods and seeds related) traits were identified. Two of these were verified in another population. The QTLs for NPPP, SNPP and NThSP formed a consensus QTL cluster on GM02. Another 27 QTLs also formed clusters in five regions. Fifteen candidate genes were mined and discussed. The results will provide more information to soybean breeding.     

Evaluation and development of flood‐tolerant soybean cultivars

Soybean (Glycine max [L.] Merr.) cultivars are generally sensitive to flooding stress. The plant growth is severely affected and grain yield is largely reduced in the flooded field. It is important to develop flood‐tolerant soybean cultivars for grain production in regions of heavy rainfalls worldwide. In this study, a total of 722 soybean genotypes were evaluated for flooding tolerance at R1 stages (first flower at any node) in the 5‐year flooding screening tests. Differential soybean genotypes exhibited diverse responses to flooding stress with that plant foliar damage score (FDS) and plant survival rate (PSR) ranged from 1.9 to 8.8 and 3.4% to 81.7%, respectively (p < .0001). Based on our standard of flooding evaluation, most genotypes were sensitive to flooding with 6.0 of average FDS and 38.7% of PSR. Fifty‐two soybean genotypes showed flooding tolerance and 11 genotypes were with consistent flooding tolerance during 4‐ to 5‐year continual evaluations. In the meantime, six genotypes were identified with consistent high sensitivity to flooding. The group analysis showed that genotypes from different sources had distinguishable responses to flooding stress (p < .0001). The interacting analysis of year and flooding tolerance indicated that FDS and PSR means were significantly different among 5 years due to weather temperature and flooding treatment time influences of each year (p < .0001). Furthermore, five breeding lines with high‐yielding and flood‐tolerant traits were developed using selected consistent flood‐tolerant and high‐yielding genotypes through conventional breeding approach.     

Association of isozyme genotypes with agronomic and seed composition traits in soybean

Summary Two crosses between Glycine max (L.) Merr. and G. soja Sieb. & Zucc. parents were used to study the association between isozyme marker loci and agronomic and seed composition traits in soybean. The parents possessed different alleles at six isozyme loci for Cross 1 (A80-244036 × PI 326581) and at eight isozyme loci for Cross 2 (A81-157007 × PI 342618A). A total of 480 BC₂F_4:6 lines from the two crosses was evaluated for 13 traits in two environments. Lines were grouped in locus classes from 0 to 5 according to the number of loci homozygous for the G. soja alleles that they possessed. Within each locus class, each isozyme genotype was represented by five random lines.Selection for G. max alleles at the isozyme loci was not effective in recovering the recurrent parent phenotype in either cross. In cross 1, however, BC₂F₄-derived lines in the 0- or 1- locus class more closely resembled the G. max parent than lines in the 4- or 5- locus classes for most of the agronomic and seed composition traits evaluated. Significant associations were found between particular isozyme genotypes and every trait analyzed. The estimated effect of genes linked to the Pgm1 locus was a delay in maturity of 6.0±3.4 days. In cross 1, the Idh2 locus was associated with a significant effect on linolenic acid content. The percentage of variation accounted for by the models of estimation varied according to the heritability of the trait. The R² was high (up to 78%) for maturity, lodging, and vining, and low (up to 21%) for seed yield. Most of the variation was associated with the BC₂F₁ family from which the lines were derived. There was little evidence that digenic epistasis was an important source of variation.Journal Paper No. J-13505 of the Iowa Agric. Home Econ. Exp. Stn., Ames, IA, Project 2475.     

Assessment of genetic diversity in synthetic hexaploid wheats and their Triticum dicoccum and Aegilops tauschii parents using AFLPs and agronomic traits

Synthetic hexaploid wheats are of interest to wheat breeding programs, especially for introducing new genes that confer resistance to biotic and abiotic stresses. A group of 54 synthetic hexaploid wheats derived from crosses between emmer wheat(Triticum dicoccum, source of the A and B genomes) and goat grass (Aegilops tauschii, D genome donor) were investigated for genetic diversity. Using the AFLP technique, dendrograms revealed clear grouping according to geographical origin for the T. dicoccum parents but no clear groups for the Ae. tauschii parents. The geographical clustering of the T. dicoccum parents was also reflected in the dendrogram of their derived synthetic hexaploids. Diversity of the T. dicoccum parents and their derived synthetic hexaploids was further evaluated by measuring 18morphological and agronomic traits on the plants. Clustering based on morphological and agronomic data also reflected geographical origin. However, comparison of genetic distances obtained from AFLP and agronomic data showed no correlation between the two diversity measurements. Nevertheless, similarities among major clusters with the two systems could be identified. Based on percentage of polymorphic markers, the synthetic hexaploids had a considerably higher level of AFLP diversity (39%) than normally observed in cultivated hexaploid wheat (12–21%). This suggests that synthetic hexaploid wheats can be used to introduce new genetic diversity into the bread wheat gene pool. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effect of pollen storage by drying and deep-freezing on the expression of different agronomic traits in maize (Zea mays L.)

Summary Pollen from the inbred maize line HMv 1645 was used to study the effect of pollen treatments (drying and deep-freezing) on the phenotypic performance of the next generation. Fresh and artificially dried pollen samples with different water contents (56%, 18%, 13% and 10%) were used for sib pollinations immediately after collection or drying. Samples containing low amounts of water were then stored in liquid nitrogen for 7 days. Fertilization ability of the samples with 13% water was the highest after storage. Plant characteristics of the next generation originated from the seeds set by differently treated (fresh, dried to 13% water and deep-frozen) pollen were examined and statistically analysed. Pollen treatments due to the pollen storage procedure did not cause detectable changes in quantitative characters of the next generation.     

Development of a cytoplasmic male‐sterile line NJCMS4A for hybrid soybean production

Cytoplasmic male‐sterile (CMS) lines are being used to produce hybrid seeds. Thus far, four CMS sources in soybean [Glycine max (L.) Merr.] have been reported in China. However, they are not sufficient or efficient in meeting the requirements of commercial soybean hybrid seed production. In this study, 33 varieties were tested for CMS using 45 crosses among 37 landraces and 17 annual wild soybean accessions (Glycine soja Sieb. et Zucc.). The cross of N23661 × N23658 showed partial to complete male sterility in backcross generations, while the corresponding reciprocal cross showed normal male fertility. Thus, the cytoplasm of N23661 is male‐sterile, the continuously backcrossed line is a male‐sterile line (designated NJCMS4A), and N23658 is its maintainer (designated NJCM4B). The male fertility of NJCMS4A was restored by another accession, Nansheng9403. Accordingly, NJCMS4A along with its maintainer and restorer composes a complete set of three lines for producing hybrid soybean. Using mitochondrial markers and sequence analyses, NJCMS4A is a CMS line with its cytoplasm not identical to the four previously reported CMS sources in soybean.     

Genetic improvement in grain yield potential and associated agronomic traits of tef (<Emphasis Type="Italic">Eragrostis tef</Emphasis>)

A yield potential experiment was conducted with one farmers variety and 10 improved varieties released over the periods 1960–1995 to estimate the progress made in improving grain yield potential and to determine changes produced on agronomic traits associated with genetic yield potential improvement. The experiment was conducted at the Debre Zeit Agricultural Research Center, Debre Zeit, Ethiopia, on two soil types in the 1997 main cropping season, using a randomized complete block design with three replications. Evaluation of cultivars from different eras in a common environment has been used to estimate breeding progress. Optimum levels of fertilizers and full weed and bird control programs were used. Netting was used to prevent lodging. Data on grain yield and its attributes were determined. Grain yield of tef was estimated to have risen for 35 years of breeding from 3425 to 4599 kg/ha. Biomass yield and kernel weight per main panicle were greater in newer cultivars, highly and linearly related to cultivar age, and positively and significantly correlated to grain yield. Number of spikelets per panicle is also greater in newer cultivars and significantly and positively correlated with grain yield. Improved plant height, panicle length and kernels per panicle were a feature of most modern genotypes. However, no change occurred in harvest index and 100-kernel weight. Results of a stepwise regression analysis of grain yield on selected yield components revealed that biomass yield was the single most important yield attribute, which accounted for 56.7% of the variation in grain yield.     

Dissection of the genetic architecture for grain quality‐related traits in three RIL populations of maize (Zea mays L.)

To manipulate the composition of the maize kernel to meet future needs, an understanding of the molecular regulation of kernel quality‐related traits is required. In this study, the quantitative trait loci (QTL) for the concentrations of grain protein, starch and oil were identified using three sets of RIL populations in three environments. The genetic maps and the initial QTL were integrated using meta‐analyses. A total of 38 QTL were identified, including 15 in population 1, 12 in population 2 and 11 in population 3. The individual effects ranged from 2.87% to 13.11% of the phenotypic variation, with seven QTL each contributing over 10%. One common QTL was found for the concentrations of grain protein and starch in bin 3.09 in the three environments and the three RIL populations. Of the 38 initial QTL, 22 were integrated into eight mQTL by meta‐analysis. mQTL3 and mQTL8 of the key mQTL in which the initial QTL displayed R² > 10% included six and three initial QTL for grain protein and starch concentrations from two or three populations, respectively. These results will provide useful information for marker‐assisted selection to improve the quality of the maize kernel.     

Genetic characterization of group A acetylsaponin‐deficient mutants from wild soybean (Glycine soja Sieb. and Zucc.)

Group A acetylsaponins are the main causative components for bitter and astringent tastes of soybean (Glycine max). In this study, we examined the genetic nature of the absence of group A acetylsaponins in 12 Korean wild soybean (Glycine soja) accessions. In all 12 accessions, the coding region (1431‐bp) of Sg‐1 locus was identical with Sg‐1^a, which adds the xylose sugar moiety at the terminal position of the C‐22 sugar chain of SS‐A, except one nucleotide (G→A change) at +948th position. This point mutation results in change of one amino acid from tryptophan (TGG) to stop codon (TGA). We observed that the mutated Sg‐1 was controlled by a single recessive gene (sg‐1^0‐a1). This gene was mapped between BARCSOYSSR_07_1561 and BARCSOYSSR_07_1598 on soybean chromosome 7. Our study demonstrated that the mutated Sg‐1 gene in Korean wild soybeans is genetically different from those identified in Japanese soybean cultivar ‘Kinusayaka’ and wild soybean JP‐36121. We believe that the new Sg‐1 mutants can also be utilized to produce a new soybean variety without bitter and astringent properties.     

Effects of photoperiod sensitivity genes Ppd‐B1 and Ppd‐D1 on spike fertility and related traits in bread wheat

Increasing grain yield is a key breeding goal in bread wheat. Several authors have suggested that a spike fertility index (SF), that is the quotient between grain number per unit spike (GNS) and spike chaff dry weight (SCDW), could be used as a yield‐related selection criterion, especially if molecular markers were available. Here, the effects of Ppd‐B1 and Ppd‐D1 genes on SFm, GNSm and SCDWm (measured at maturity) and the relationship between these variables were analysed in field experiments carried out during three crop seasons at Balcarce, Argentina, on an association mapping population of 100 bread wheat cultivars of diverse origin released in Argentina between 1927 and 2010. Results show that both Ppd‐B1 and Ppd‐D1 are associated with SFm with similar effects. Cultivars with insensitive alleles at both genes showed a mean SFm 9.2% greater than those with sensitive alleles at both genes; at each gene, difference in SFm between insensitive and sensitive alleles was ~4.5%. In turn, each gene showed a differential effect on GNSm and SCDWm, as Ppd‐B1 was more related to SCDWm, whereas Ppd‐D1 was only related to GNSm. Although more research needs to be carried out in order to ascertain the physiological pathway by which these genes affect spike fertility, this study represents a first approximation in order to elucidate the molecular and genetic basis underlying SF and related physiological traits.     

Changes in photo‐thermal sensitivity of widely grown Chinese soybean cultivars due to a century of genetic improvement

Photo‐thermal sensitivity is a crucial factor that determines the phenology, adaptation and yield production of soybean. However, the change of photo‐thermal sensitivity due to a long process of soybean breeding remains unknown. To better understand this unique characteristic of soybean, we sought to evaluate the genetic improvement in photo‐thermal sensitivity of 63 widely grown soybean cultivars, spanning 83 years of breeding (1923–2006), from four main subregions in China. Days to the first flower was measured, and photo‐thermal sensitivity was calculated. We found that photo‐thermal sensitivity of cultivars in the northern Heilongjiang (NH) region showed a quadratic relationship with year of release. However, photo‐thermal sensitivity was negatively correlated with year of release in the Huang‐Huai‐Hai Valley (HH) region. There were no significant trends of change found in the mid‐southern Heilongjiang (MSH) and Jilin and Liaoning (JL) regions. The changing trend of photo‐thermal sensitivity was relatively consistent across different environments, particularly in the NH and HH regions (photoperiod, temperature or planting year). The insensitivity to photo‐thermal condition provided an advantage for modern cultivars to achieve broad adaptation.     

Meta‐analysis and overview analysis of quantitative trait locis associated with fatty acid content in soybean for candidate gene mining

As soybean seed fatty acid content is valued in food, animal feed and some industrial applications, plant breeders continually aim to improve seed fatty acid constituent value. This study analysed 163 original quantitative trait loci (QTLs) related to soybean fatty acid content from databases and references and revealed 43 consensus QTLs. Meta‐analysis using BioMercator ver.2.1 indicated that these were located across 16 linkage groups (LGs) excluding LG D1a, LG C1, LG M and LG H. Moreover, the overview method was used to optimize these QTLs based on statistical analysis. Some valid QTL regions were narrowed down to 0.5 Mb and mapped on the same LGs as the meta‐analysis result. Furthermore, the functions of all genes located in these consensus QTL intervals were predicted and eight candidate genes were identified. KEGG pathway analysis indicated that Glyma.13G127900 and Glyma.18G232000 were involved in the fatty acid synthesis metabolic (pathway ID ko00071, ko00062, ko01040). These results lay a foundation for fine mapping of QTLs related to fatty acid content and marker‐assisted breeding in soybean.     

Identification and characterization of new S‐alleles associated with self‐incompatibility in almond

Almond is a highly heterozygous species with a high number of S‐alleles controlling its gametophytic self‐incompatibility system (GSI). In this work, we have analysed 14 Spanish local almond cultivars for S‐RNase allele diversity. Five new S‐RNase alleles were identified by cloning and sequencing, S₃₁ (804 bp) in ‘Pou de Felanitx’ and ‘Totsol’, S₃₂ (855 bp) in ‘Taiatona’, S₃₃ (1165 bp) in ‘Pou d’Establiments’ and ‘Muel’, S₃₄ (1663 bp) in ‘Pané‐Barquets’ and S₃₅ (1658 bp) in ‘Planeta de les Garrigues’. Additionally, seven already known almond alleles could be recognized in the local cultivars studied. The high number of new alleles identified reveals the wide diversity of almond germplasm still existing and requiring characterization, and points to the possibility of new findings by a wider study focusing on other provenances. The almond S‐RNases have been compared to those of other Prunus species, showing a high identity and confirming that the S‐RNase gene in this genus presents a probable common ancestor.     

Construction of chromosomal segment substitution lines and genetic dissection of introgressed segments associated with yield determination in the parents of a super‐hybrid rice

Heterosis is a phenomenon whereby hybrids of inbred lines produce favourable phenotypes that exceed those of their parents. Traits of interest are higher yield and stronger stress tolerance. The two‐line super‐hybrid rice ‘Liangyoupei9’ (LYP9) shows superiority to both its elite inbred line ‘93‐11’ and ‘Pei'ai64s’ (‘PA64s’) parents and conventional hybrids. However, the genetic basis of its hybrid vigour, especially yield determination, remains elusive. In the present study, a set of 156 chromosome segment substitution lines (CSSLs) carrying overlapping segments from ‘PA64s’ in a genetic background of ‘93‐11’ were constructed and planted in six environments. Three major agronomic traits, viz. panicle length (PL), heading date (HD) and plant height (PH), and five yield‐related traits, viz. grain weight per panicle (GWP), number of grains per panicle (GPP), 1000‐grain weight (TGW), seed set (SS) and number of panicles of per plant (PPP), were evaluated over 3 years. Quantitative trait loci (QTL) analysis was conducted using a likelihood ratio test based on stepwise regression. Forty‐six putative QTL distributed on 11 chromosomes were detected in more than one year. Remarkably, GWP of four CSSLs carrying positive yield QTL outperformed the recurrent parent ‘93‐11’ by more than 15%, in at least two environments. These results indicate that CSSLs are effective in identifying yield‐associated traits, and lines harbouring such QTL will be rich in resources for future molecular breeding programmes.     

Detection of epistatic and environmental interaction QTLs for leaf orientation‐related traits in maize

Leaf architecture traits in maize are quantitative and have been studied by quantitative trait loci (QTLs) mapping. However, additional QTLs for these traits require mapping and the interactions between mapped QTLs require studying because of the complicated genetic nature of these traits. To detect common QTLs and to find new ones, we investigated the maize traits of leaf angle, leaf flagging‐point length, leaf length and leaf orientation value using a set of recombinant inbred line populations and single nucleotide polymorphism markers. In total, 19 QTLs contributed 4.13–13.52% of the phenotypic effects to the corresponding traits that were mapped, and their candidate genes are provided. Common and major QTLs have also been detected. All of the QTLs showed significant additive effects and non‐significant additive × environment effects in combined environments. The majority showed additive × additive epistasis effects and non‐significant QTL × environment effects under single environments. Common and major QTLs provided information for fine mapping and gene cloning, and SNP markers can be used for marker‐assisted selection breeding.     

Phenotypic variation in root architecture traits and their relationship with eco-geographical and agronomic features in a core collection of tetraploid wheat landraces (<Emphasis Type="Italic">Triticum turgidum</Emphasis> L.)

To obtain varieties with root systems adapted to marginal environments it is necessary to search for new genotypes in genetically diverse materials, such as landraces that are more likely to carry novel alleles for different root features. A core collection of ‘durum’ wheat, including three subspecies (dicoccon, turgidum and durum) from contrasting eco-geographical zones, was evaluated for root traits and shoot weight at the seminal root stage. Distinctive rooting phenotypes were characterized within each subspecies, mainly in subsp. durum. Contrasting rooting types, including large roots with shallow distributions, and others with high root numbers were identified. Correlations with climatic traits showed that root shape is more relevant in adaptation to eco-geographical zones in subsp. dicoccon, whereas in subsp. turgidum and durum, which come from warmer and drier areas, both size and shape of roots could have adaptive roles. Root traits with the largest positive effects on certain yield components under limited water conditions included root diameter in subsp. dicoccon, root size in turgidum, and root number in durum. Additionally, shoot weight at the seedling stage had important effects in subsp. turgidum and durum. Twenty-eight marker–trait associations (MTAs) previously identified in this collection for agronomic or quality traits were associated with seminal root traits. Some markers were associated with only one root trait, but others were associated with up to six traits. These MTAs and the genetic variability characterized for root traits in this collection can be exploited in further work to improve drought tolerance and resource capture in wheat.     

The relation between grain yield and some related traits of spring barley (Hordeum vulgare L.) and their usefulness in a breeding program

Summary The objective of this study was to evaluate traits which can facilitate and improve selection for grain yield of spring barley. Five experiments were conducted in different environments to measure grain yield and yield related traits of breeding lines and exotic varieties. Differences for rate of canopy expansion were significant and offer the opportunity to select for a high weed suppressing potential but there was no relation to grain yield. Dry matter yield/m² at anthesis and its water-soluble-carbohydrate content were not correlated with grain yield/m² and number of grains/m². Variation in biomass among breeding lines with a similar development and plant height was small. Biomass standardized for plant height was stable across environments and showed a good correlation with number of grains and grain yield. The contribution of pre-anthesis assimilation to grain yield was only important under low yielding experimental conditions, but the differences among the genotypes for this trait were inconsistent. It may be difficult to select genotypes with a high potential contribution of pre-anthesis assimilation to grain yield.