Identification of QTL controlling post-flowering period in soybean

The length of the reproductive period affects the grain yield of soybean (Glycine max [L.] Merr), and genetic control of the period might contribute to yield improvement. To detect genetic factor(s) controlling the reproductive period, a population of recombinant inbred lines (RILs) was developed from a cross between Japanese landrace ‘Ippon-Sangoh’ and, Japanese cultivar ‘Fukuyutaka’ which differ in their duration from flowering to maturation (DFM) relative to the difference in the duration from sowing to flowering (DSF). In the RIL population, the DFM correlated poorly (r = −0.16 to 0.34) with the DSF in all field trials over 3 years. Two stable QTLs for the DFM on chromosomes (Chr-) 10 and 11 as well as two stable QTLs for the DSF on Chr-10 and -16 were identified. The QTL on Chr-11 for the reproductive period (designated as qDfm1; quantitative trait locus for duration from flowering to maturation 1) affected all three trials, and the difference in the DFM between the Fukuyutaka and Ippon-Sangoh was mainly accounted for qDfm1, in which the Fukuyutaka allele promoted a longer period. qDfm1 affected predominantly the reproductive period, and thus it might be possible to alter the period with little influence on the vegetative period.     

Development and evaluation of chromosome segment substitution lines (CSSLs) carrying chromosome segments derived from Oryza rufipogon in the genetic background of Oryza sativa L.

The wild relatives of rice (Oryza sativa L.) are useful sources of alleles that have evolved to adapt in diverse environments around the world. Oryza rufipogon, the known progenitor of the cultivated rice, harbors genes that have been lost in cultivated varieties through domestication or evolution. This makes O. rufipogon an ideal source of value-added traits that can be utilized to improve the existing rice cultivars. To explore the potential of the rice progenitor as a genetic resource for improving O. sativa, 33 chromosome segment substitution lines (CSSLs) of O. rufipogon (W0106) in the background of the elite japonica cultivar Koshihikari were developed and evaluated for several agronomic traits. Over 90% of the entire genome was introgressed from the donor parent into the CSSLs. A total of 99 putative QTLs were detected, of which 15 were identified as major effective QTLs that have significantly large effects on the traits examined. Among the 15 major effective QTLs, a QTL on chromosome 10 showed a remarkable positive effect on the number of grains per panicle. Comparison of the putative QTLs identified in this study and previous studies indicated a wide genetic diversity between O. rufipogon accessions.     

Genome-wide association study of yield components and fibre quality traits in a cotton germplasm diversity panel

A genome-wide association study (GWAS) was conducted on a diversity panel of 103 cotton accessions over three seasons to determine genetic contributions to a range of cotton yield components including fibre quality, plant architecture and stomatal conductance traits. The accessions covered breeding lines, released cultivars and some obsolete cultivars that contributed significantly to modern breeding pools. They were genotyped with Illumina’s CottonSNP63 K single nucleotide polymorphism (SNP) assay. Broad-sense heritability was low for yield component traits (\(h_{B}^{2}\) = 0.14–0.43), except for gin turnout and boll weight (\(h_{B}^{2}\)) = 0.74 and 0.59, respectively), and low to high for fibre quality traits (\(h_{B}^{2}\) = 0.26–0.89). Population structure analysis revealed extensive admixture and cryptic relatedness amongst the accessions. Genome-wide linkage disequilibrium (LD) analyses showed LD decayed, on average, within a physical distance of 5 Mbp and reduced to 2 Mbp at r ² ≥ 0.2, suggesting that few markers are necessary for association mapping in cotton. A mixed linear model accounting for population structure and cryptic relatedness identified 17 and 50 significant SNP associations for fibre length and micronaire, respectively. GWAS failed to detect significant associations in other traits, with the contribution of any single SNP to the phenotypic falling below 5%. This may be due to the low level of DNA polymorphism in cotton and/or insufficient resolution provided by the cotton SNP chip. Whole genome sequencing combined with whole genomic selection approaches that do not require prior knowledge about the effect or function of individual SNPs may be better suited than GWAS for trait dissection and prediction in cotton breeding.     

WIPPER: an accurate and efficient field phenotyping platform for large-scale applications

More accurate, rapid, and easy phenotyping tools are required to match the recent advances in high-throughput genotyping for accelerating breeding and genetic analysis. The conventional data recording in field notebooks and then inputting data to computers for further analysis is inefficient, time-consuming, laborious, and prone to human error. Here, we report WIPPER (for Wireless Plant Phenotyper), a new phenotyping platform that combines field phenotyping and data recording with the aid of Bluetooth communication, thus saving time and labor not only for field data recoding but also for inputting data to computers. Additionally, it eliminates the risk of human error associated with phenotyping and inputting data. We applied WIPPER to 100 individuals of a rice recombinant inbred line (RIL) for measuring leaf width and relative chlorophyll content (SPAD value), and were able to record an accurate data in a significantly reduced time compared with the conventional method of data collection. We are currently using WIPPER for routine management of rice germplasm including recording and documenting information on phenotypic data, seeds, and DNA for their accelerated utilization in crop breeding.     

Development of EST-SSR markers and construction of a linkage map in faba bean (Vicia faba)

To develop a high density linkage map in faba bean, a total of 1,363 FBES (Faba bean expressed sequence tag [EST]-derived simple sequence repeat [SSR]) markers were designed based on 5,090 non-redundant ESTs developed in this study. A total of 109 plants of a ‘Nubaria 2’ × ‘Misr 3’ F₂ mapping population were used for map construction. Because the parents were not pure homozygous lines, the 109 F₂ plants were divided into three subpopulations according to the original F₁ plants. Linkage groups (LGs) generated in each subpopulation were integrated by commonly mapped markers. The integrated ‘Nubaria 2’ × ‘Misr 3’ map consisted of six LGs, representing a total length of 684.7 cM, with 552 loci. Of the mapped loci, 47% were generated from multi-loci diagnostic (MLD) markers. Alignment of homologous sequence pairs along each linkage group revealed obvious syntenic relationships between LGs in faba bean and the genomes of two model legumes, Lotus japonicus and Medicago truncatula. In a polymorphic analysis with ten Egyptian faba bean varieties, 78.9% (384/487) of the FBES markers showed polymorphisms. Along with the EST-SSR markers, the dense map developed in this study is expected to accelerate marker assisted breeding in faba bean.     

Breeding opportunities for early,free-threshing and semi-dwarf <Emphasis Type="Italic">Triticum monococcum</Emphasis> L.

Einkorn wheat, Triticum monococcum L. (2n = 2x = 14, A^mA^m genome), is a primitive, cultivated form of diploid wheat. The shortcoming of einkorn is that it lacks the free-threshing habit. Early heading and semi-dwarf traits are also required to fit modern agricultural practice. In the present study we developed T. monococcum pre-breeding germplasm having early, free threshing traits by utilizing an early heading source, two sources of soft glume (spike) and three sources of semi-dwarfism to combine their phenotypes into pre-breeding materials. We found two different genes determined free threshing of einkorn wheat. One of them was the sog (soft glume) gene from Triticum sinskajae Filat. et Kurkiev (2n = 2x = 14, A^mA^m genome) and another was the sos (soft spike) gene, which was completely linked or pleiotropic with the gene for semi-dwarfism. The genes sos, spd (short peduncle) and sd17654 (semi-dwarf CItr 17654) were utilized to develop semi-dwarf T. monococcum lines. Field performance of 6 early and free-threshing pre-breeding materials with sos and spd genes were tested over three crop seasons. Five semi-dwarf pre-breeding materials (PBMs) were obtained. However, these materials had slightly less grain yield than #252 (tall and hulled check) and PBM-1 (tall free-threshing check). Harvest index of the pre-breeding materials was improved due to the presence of sos and spd genes. If optimized cultivation practice is performed, these pre-breeding materials can be utilized as sources of early, free-threshing and semi-dwarf traits to produce modern T. monococcum varieties.     

Application of half-sib mating for genetic analysis of forage yield and related traits in Bromus inermis

Despite efforts made, forage yield of smooth bromegrass has increased slowly over the last 50 years of breeding. It therefore seems necessary to investigate more on the genetic basis of agro-morphological traits in this cool-season, highly drought resistant grass. The present study was aimed at estimation of total genetic variance, narrow-sense heritability, general combining ability, phenotypic and genotypic correlation among different quantitative traits in half-sib (HS) families derived from polycross of 25 smooth bromegrass genotypes that were mainly originated from Iran. Families differed significantly for all of the agro-morphological and quality traits measured. Narrow sense heritability ( ${\text{h}}_{\text{n}}^{2}$ ) ranged from about 0.2 (plant height) to 0.7 (day to inflorescence emergence and day to anthesis). Moderate to high heritability for forage dry matter yield (0.42) indicates that phenotypic selection for this trait can be successful. A wide range of general combining ability was observed for most of the studied traits, especially those related to forage yield. Relatively low genetic variation and heritability for crude protein and also negative correlation of this trait with forage yield, indicates a low probability of improving forage yield and quality simultaneously.     

Genetic and phenotypic parameters in common bean segregant populations from intra and inter-gene pool crosses of elite lines

This study aimed compare segregating populations of common bean (Phaseolus vulgaris L.) derived from intra and inter-gene pool crosses of elite lines by estimates of some genetic and phenotypic parameters. Four elite lines highly adapted to Brazilian conditions were used (ESAL 686 and BRS Radiante: Andean gene pool; BRSMG Majestoso and BRS Valente: Mesoamerican gene pool). Two intra-gene pool (“A”: ESAL 686 × BRS Radiante; “B”: BRS Valente × BRSMG Majestoso) and two inter-gene pool segregant populations (“C”: BRS Radiante × BRSMG Majestoso and “D”: ESAL 686 × BRS Valente) were obtained. The parental lines, the cultivar Pérola and fifty-five F_2:3 progenies of each population were evaluated in the rainy season 2010/2011, and afterwards (F_2:4) in dry season of 2011. Estimates of genetic variance ( $\hat{\sigma }_{G}^{2}$ ), heritability on a progeny mean basis ( $\hat{h}_{p}^{2}$ ), heritability realized ( $\hat{h}_{R}^{2}$ ) and gain expected from selection (GS) were obtained at joint analysis, in each population, for the traits number of days to flowering (DTF), 100 seed weight (100SW) and seed yield (SYD). It was observed that for all traits, inter-gene pool crosses (“C” and “D”) showed higher estimates of $\hat{\sigma }_{G}^{2}$ , $\hat{h}_{p}^{2}$ , $\hat{h}_{R}^{2}$ and GS than intra-gene pool crosses (“A” and “B”), which indicates more genetic variability. However, for SYD, the higher variability was associated to lower average of seed yield, showing that even utilizing adapted parents the inter-gene pool crosses are inferior to crosses between lines of the same gene pool.     

Construction of integrated linkage map of a recombinant inbred line population of white lupin (Lupinus albus L.)

We report the development of a Diversity Arrays Technology (DArT) marker panel and its utilisation in the development of an integrated genetic linkage map of white lupin (Lupinus albus L.) using an F₈ recombinant inbred line population derived from Kiev Mutant/{"type":"entrez-protein","attrs":{"text":"P27174","term_id":"14195583","term_text":"P27174"}}P27174. One hundred and thirty-six DArT markers were merged into the first genetic linkage map composed of 220 amplified fragment length polymorphisms (AFLPs) and 105 genic markers. The integrated map consists of 38 linkage groups of 441 markers and spans a total length of 2,169 cM, with an average interval size of 4.6 cM. The DArT markers exhibited good genome coverage and were associated with previously identified genic and AFLP markers linked with quantitative trait loci for anthracnose resistance, flowering time and alkaloid content. The improved genetic linkage map of white lupin will aid in the identification of markers for traits of interest and future syntenic studies.     

The breeding of diploid cultivars of Cyclamen persicum

1. 1.
   Most cultivars of Cyclamen persicum are autotetraploids. This implies that true breeding cultivars cannot be obtained by ordinary pedigree selection. Theoretically it could be done by repeated pedigree selection in groups of F₄-lines, descended from one F₃-line and from one F₂-plant, or, expressed in other words, by testing part of the F₂-plants not only in F₃, but also in F₄. It is demonstrated that such a procedure is practically impossible by the large numbers of necessary plants. Therefore, the building up of a complete collection of diploid cultivars is necessary.     
   
   

Genetic parameters and selection gains in early clonal evaluation trials: implications for cassava breeding

The objective of this study was to estimate and compare genetic parameters in early cassava breeding phases (clonal evaluation trials—CET and preliminary yield trials—PYT) in full-sib (F₁) and self-pollinated (S₁) families, besides estimating the genetic gains. Twenty-three F₁ and six S₁ families were evaluated using the augmented block design in CET and the randomized complete block design in PYT for fresh root yield (FRY), root dry matter content (DMC) and starch yield (STY). In CET, most of the variance was due to environmental (\(\sigma_{e}^{2}\)) followed by variance within F₁ and S₁ (\(\sigma_{Clone/Fam}^{2}\)) families, with the exception of DMC in S₁ families. PYT presented the opposite behavior. In contrast, specifically for S₁ families, the variance between families (\(\sigma_{ Fam}^{2}\)) was more important than \(\sigma_{e}^{2}\) and \(\sigma_{Clone/Fam}^{2}\) in PYT. The heritability of families (\(h_{Fam}^{2}\)) was lower than individual broad-sense heritability (\(h_{g}^{2}\)) in all trials and families. Regardless of the family type and trial, family accuracy (\(r_{ggFam}\)) was lower than the clone accuracies (\(r_{ggCl}\)). Predicted gains using the selection index (SI) applied to best linear unbiased prediction (BLUP) were higher in PYT compared with CET and higher in F₁ families in comparison with S₁. There was also low coincidence in clone selection in both trials (30 and 45% for F₁ and S₁ families, respectively). For cassava breeding, it is recommended to obtain a higher number of clones per family and to use the SI with moderate intensity, particularly in CET.     

QTL mapping in diploid potato by using selfed progenies of the cross <Emphasis Type="Italic">S. tuberosum</Emphasis> × <Emphasis Type="Italic">S. chacoense</Emphasis>

Usually, mapping studies in potato are performed with segregating populations from crosses between highly heterozygous diploid or tetraploid parents. These studies are hampered by a high level of genetic background noise due to the numerous segregating alleles, with a maximum of eight per locus. In the present study, we aimed to increase the mapping efficiency by using progenies from diploid inbred populations in which at most two alleles segregate. Selfed progenies were generated from a cross between S. tuberosum (D2; a highly heterozygous diploid) and S. chacoense (DS; a homozygous diploid clone) containing the self-incompatibility overcoming S locus inhibitor (Sli-gene). The Sli-gene enables self-pollination and the generation of selfed progenies. One F2 population was used to map several quality traits, such as tuber shape, flesh and skin color. Quantitative trait loci were identified for almost all traits under investigation. The identified loci partially coincided with known mapped loci and partially identified new loci. Nine F3 populations were used to validate the QTLs and monitor the overall increase in the homozygosity level.     

Quantitative trait loci affecting intensity of violet flower colour in potato

Anthocyanins occur in potato tuber skin and flesh, sprouts, leaves, stems and flowers. The goal of this study was to identify genomic regions and candidate gene alleles key for accumulation of anthocyanins in potato corolla in various quantities. QTL analyses were performed in two mapping populations segregating for flower colour intensity and candidate genes were identified on the basis of function and location (chalcone isomerase, chi; chalcone synthase, chs) or location (RNA-dependent RNA polymerase 1, RDR1). We detected three and four QTL affecting the violet flower colour intensity using the two mapping populations, respectively. In both populations a locus F, necessary for violet flower colour, segregated and we used different approaches to differentiate the qualitative effect of this locus and to detect the genetic factors affecting the quantitative flower colour intensity. The strongest QTL and the only one common for the two mapping populations was located on chromosome V. The role of all three candidate genes, chi, chs and RDR1, in control of flower colour intensity is supported to different extents by the performed genetic analyses. The most important QTL on chromosome V is most likely in the same position as the QTL for anthocyanin tuber flesh coloration described previously, which indicates that the natural variation in some biosynthetic and/or regulatory genes may influence anthocyanin levels in multiple tissues.     

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.     

Genetic parameters for growth traits and stem-straightness in <Emphasis Type="Italic">Eucalyptus urophylla</Emphasis> × <Emphasis Type="Italic">E. camaldulensis</Emphasis> hybrids from a reciprocal mating design

An inter-specific hybrid breeding program involving Eucalyptus urophylla (U) and Eucalyptus camaldulensis (C) was implemented in order to provide genotypes better adapted to southern China with improved growth rate, stem-straightness and wind-resistance. A trial involving 36 reciprocal crosses from six parents each of C and U that had been preselected for superior growth and stem-straightness was established at a site in Luokeng in Guangdong province. Ten, pure-species families using the hybrid parents as open-pollinated female parents were included as controls. Survival and growth traits at ages 2 and 8.3 years and stem-straightness at age 2 years were assessed. Inter-specific hybrids generally performed better than the pure species in terms of survival, growth traits and stem-straightness. Female U by male C crosses generally outperformed those involving male U and female C. Further indication of the significant reciprocal effect was supported by negative and low correlations between paired groups of full-sibs that differed only in the direction of the cross. Components of female additive genetic variance and narrow-sense heritability calculated from this estimate (\(\sigma_{\rm Af}^{2}\) and \(h_{\rm f}^{2}\)), respectively) were generally higher than those of the male \(\left( {\sigma_{\rm Am,}^{2} h_{\rm m}^{2} } \right)\), providing evidence for maternal effects. The narrow-sense heritability (h²) estimates based on general hybridizing ability for growth traits and stem-straightness were generally low at both ages, and of low precision at 8.3 years. The ratio of hybrid additive-to-dominance variance \(\left( {{{\sigma_{\rm A}^{2} } \mathord{\left/ {\vphantom {{\sigma_{\rm A}^{2} } {\sigma_{\rm D}^{2} }}} \right. \kern-0pt} {\sigma_{\rm D}^{2} }}} \right)\) was of little practical consequence at age 2 years and had further decreased by age 8.3 years. Trait-trait genetic correlations amongst hybrids were generally positive and moderate to high. Hybrid vigour, gauged by comparison with the performance of the pure species progeny was significant, though correlations between pure species and hybrid progeny-based estimates of parental performance were weak, indicating that making parental selections in pure species trials may not be a successful strategy.     

Genetic mapping of resistance to <Emphasis Type="Italic">Puccinia hordei</Emphasis> in three barley doubled-haploid populations

The success of breeding for barley leaf rust (BLR) resistance relies on regular discovery, characterization and mapping of new resistance sources. Greenhouse and field studies revealed that the barley cultivars Baronesse, Patty and RAH1995 carry good levels of adult plant resistance (APR) to BLR. Doubled haploid populations [(Baronesse/Stirling (B/S), Patty/Tallon (P/T) and RAH1995/Baudin (R/B)] were investigated in this study to understand inheritance and map resistance to BLR. The seedlings of two populations (B/S and R/B) segregated for leaf rust response that conformed to a single gene ratio (\({\text{X}}_{1:1}^{2}\) = 0.12, P > 0.7 for B/S and \({\text{X}}_{1:1}^{2}\) = 0.34, P > 0.5 for R/B) whereas seedlings of third population (P/T) segregated for two-gene ratio (\({\text{X}}_{1:1}^{2}\) = 0.17, P > 0.6) when tested in greenhouse. It was concluded that the single gene in Baudin and one of the two genes in Tallon is likely Rph12, whereas gene responsible for seedling resistance in Stirling is Rph9.am (allele of Rph12). The second seedling gene in Tallon is uncharacterized. In the field, APR was noted in lines that were susceptible as seedlings. A range of disease responses (CI 5–90) was observed in all three populations. Marker trait association analysis detected three QTLs each in populations B/S (QRph.sun-2H.1, QRph.sun-5H.1 and QRph.sun-6H.1) and R/B (QRph.sun-1H, QRph.sun-2H.2, QRph.sun-3H and QRph.sun-6H.2), and four QTLs in population P/T (QRph.sun-6H.2, QRph.sun-1H.2, QRph.sun-5H.2 and QRph.sun-7H) that significantly contributed to low leaf rust disease coefficients. High frequency of QRph. sun-5H.1, QRph. sun-6H.1, QRph. sun-1H.1, QRph. sun-2H.2, QRph. sun-6H.2, QRph. sun-7H (based on presence of the marker, closely associated to the respective QTLs) was observed in international commercial barley germplasm and hence providing an opportunity for rapid integration into breeding programmes. The identified candidate markers closely linked to these QTLs will assist in selecting and assembling new APR gene combinations; expectantly this will help in achieving good levels of durable resistance for controlling BLR.     

Genetic dissection of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) tiller,plant height,and grain yield based on QTL mapping and metaanalysis

Tiller number per plant (TN) and plant height (PH) are important agronomic traits related to grain yield (GY) in rice (Oryza sativa L.). A total of 30 additive quantitative trait loci (A-QTL) and 9 significant additive × environment interaction QTLs (AE-QTL) were detected, while the phenotypic and QTL correlations confirmed the intrinsic relationship of the three traits. These QTLs were integrated with 986 QTLs from previous studies by metaanalysis. Consensus maps contained 7156 markers for a total map length of 1112.71 cM, onto which 863 QTLs were projected; 78 meta-QTLs (MQTLs) covering 11 of the 30 QTLs were detected from the cross between Dongnong422 and Kongyu131 in this study. A total of 705 predicted genes were distributed over the 21 MQTL intervals with physical length <0.3 Mb; 13 of the 21 MQTLs, and 34 candidate genes related to grain yield and plant development, were screened. Five major QTLs, viz. qGY6-2, qPH7-2, qPH6-3, qTN6-1, and qTN7-1, were not detected in the MQTL intervals and could be used as newly discovered QTLs. Candidate genes within these QTL intervals will play a meaningful role in molecular marker-assisted selection and map-based cloning of rice TN, PH, and GY.     

Identification and fine mapping of molecular markers closely linked to fruit spines size <Emphasis Type="Italic">ss</Emphasis> gene in cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L.)

Fruit spine size is one of the importantly external quality traits effected the economic value of cucumber fruit. Morphological–cytological observation of the fruit spine size phenotype indicated that large spine formation arises from an increasing of spiny pedestal cell number caused by cell division, and best periods to accurately score fruit spine size trait was 4th day before flowering to 7th day after flowering according the continuous observation. Genetic analysis showed that a single dominant gene determined the fruit spine size trait in cucumber. BC₁ population (189 individuals) of two inbred lines (large spine PI197088 and small spine SA0422) was used for primary mapping of the SS/ss locus with 7 markers covering an interval of 37.1 cM. An F₂ segregating population of 1032 individuals constructed from the same two parents (PI197088 and SA0422) was used to fine mapping of the SS/ss locus. Six new markers linked to the gene were successfully screened for construction of a fine linkage map, in which the SS/ss locus was located in the region flanked by marker SE1 (3 recombinants) and SSR43 (2 recombinants) with a 189 kb physical distance. Markers from this study will be valuable for candidate gene cloning and marker-assisted selection for cucumber breeding.