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.     

Inoculation with ascospores of Sclerotinia trifoliorum for detection of clover rot resistant red clover

Breeding red clover for resistance to clover rot by mycelial inoculation presents many difficulties. It was investigated whether an other method of infection, viz. ascospore inoculation, would yield better results.

From the investigations the following conclusions can be drawn:

1. 1.

   Raising apothecia on a large scale and inoculating clover plants with the ascospores is a simple procedure.

2. 2.

   Ascospore dispersion can be stimulated by allowing a cold air current over the ripe apothecia.

3. 3.

   The degree of susceptibility of red clover varieties cannot be inferred from the density of brown spots in the leaves, caused with ascospore infection.

4. 4.

   One field experiment with varieties and families, and an experiment in a chamber and in a frame, the latter two with varieties only, did not demonstrate that ascospore inoculation revealed the resistance better than the customary mycelial infection. By operating in a chamber or in a frame the rotting in clover necessary for selection purposes, can be produced in the properest way be mycelial inoculation. In the open a combination of mycelial and ascospore inoculation is recommended because under these circumstances there is a greater chance that the desired degree of rotting occurs.

5. 5.

   With mycelial inoculation some varieties appeared to possess an other susceptibility to clover rot than when ascospore inoculation was applied. A possible explanation of this phenomenon was given.

     

Factors influencing the occurrence of clubroot in semi-resistant populations of Brassica oleracea L.

1. 1.
   In breeding for resistanceto clubroot the plants have to be exposed to infection as long as possible. The clubbing of a susceptible variety forms an unreliable measure of the efficiency of the clubroot test.     
   
   

Hybrid breeding in early spring cabbage

1. 1.
   From 1958 to 1962 research was carried out on the breeding of hybrid varieties of pointed-headed cabbage.     
   
   

A proposed classification of screening methods for plant breeding programs

The importance of screening in a plant breeding program is discussed. A systematic classification of screening methods is proposed based on increasing order of difficulty. Method I. Direct identification

1. Ia.
   Visual inspection involving gross morphological characters.     
   
   

The inheritance of mildew resistance in progenies of the cultivated apple

1. 1.
   Resistance to Apple Mildew (Podosphaera leucotricha) is shown to be inherited quantitatively and apple varieties vary in the resistance contribution which they pass on to their progeny.     
   
   

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.     

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.     

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.     

The selection of pulses in suriname

The selection of pulses in Suriname can be distinguished according as the objective is aiming at breeding for sandy soils or for heavy clay soils. The selection for sandy soils is mainly related to groundnuts for local consumption. This article deals with selection for heavy clay soils where pulses are grown in rotation with rice and are destined mainly for the world market. The crops are soybeans, cowpeas, blackeye peas, mungbeans and some other, minor crops. The existing local varieties were partly superseded by varieties from Indonesia or the Philippines, partly by lines selected from local varieties. The results of the investigations led to the following conclusions.

1. 1.
   Any country wishing to raise varieties that surpass its own local varicties can start with simple line selection.     
   
   

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.     
   
   

Are tree breeders properly predicting genetic gain? A case study involving <Emphasis Type="Italic">Corymbia</Emphasis> species

The estimation of quantitative genetic parameters in breeding programs is important to ensure efficient selection. In this context, knowledge of the mating system is critical, as it underpins assumptions about inter-relatedness on which variance component estimation depends. However, proper account of the breeding system is not always taken, either because it is unknown and/or because it is ignored. That eucalypts have a mixed-mating system is well-established, however many breeders use models that assume outcrossed mating with an infinite number of male parents (i.e. allogamous mating), from which genetic parameter estimates are then used to predict genetic gains. First-generation, open-pollinated progeny tests of Corymbia citriodora subsp. citriodora and C. citriodora subsp. variegata, being managed for seed production, were used to investigate the likely bias, resulting in overestimation of genetic parameters under the assumption of allogamous mating. When we assumed allogamous mating, we observed inflated predictions of additive variance and narrow-sense heritability (\(\hat{h}_{a}^{2}\)) of diameter at breast height and height. The overestimate of \(\hat{h}_{a}^{2}\) was approximately 32% for C. citriodora subsp. citriodora and 21% for C. citriodora subsp. variegata. Inappropriate modelling of relatedness in eucalypts that assumes panmictic outcrossing when in fact these species have a mixed-mating system results in overestimates of the population genetic gain with selection.     

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.     

Analysis of a major rice blast resistance gene in the rice restorer line Hanghui 1179

Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most devastating diseases of rice (Oryza sativa) worldwide. Identification and utilization of resistance genes in rice breeding is considered to be an effective and economical method to control this disease. Hanghui 1179 (HH1179) is a new native rice restorer line developed in South China. The hybrids derived from HH1179 show broad-spectrum resistance against rice blast in South China, and a further understanding of the genetic resistance in HH1179 will provide useful information for breeding resistant cultivars. In the present study, we used bulked segregant analysis combined with specific-length amplified fragment sequencing to identify a dominant gene from HH1179 that provides resistance against the rice blast isolate GD13-14. Association analysis indicated that the resistance gene is located on chromosome 6 and we mapped the target gene to a 100.8 kb region (between markers InDel-8 and RM19818) that contains the Pi2/Pi9/Piz/Piz-t/Pi50 gene cluster. Candidate gene prediction and cDNA sequencing indicated that the target resistance gene in HH1179 is Pi2. Our findings will be valuable for resistance breeding with restorer line HH1179.     

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.     

Rubber tree early selection for yield stability in time and among locations

Rubber production in the rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] can be expressed differently in different environments. Thus the objective of the present study was to select productive progenies, stable and responsive in time and among locations. Thirty progenies were assessed by early yield tests at three ages and in three locations. A randomized block design was used with three replications and ten plants per plot, in 3 × 3 m spacing. The procedure of the mixed linear Reml/Blup model—restricted maximum likelihood/best non-biased linear prediction was used in the genetic statistical analyses. In all the individual analyses, the values observed for the progeny average heritability ( $ \hat{h}_{pa}^{2} $ ) were greater than those of the additive effect based on single individuals ( $ \hat{h}_{a}^{2} $ ) and within plot additive ( $ \hat{h}_{ad}^{2} $ ). In the joint analyses in time, there was genotype × test interaction in the three locations. When 20 % of the best progenies were selected the predicted genetic gains were: Colina G_G = 24.63 %, Selvíria G_G = 13.63 %, and Votuporanga G_G = 25.39 %. Two progenies were among the best in the analyses in the time and between locations. In the joint analysis among locations there was only genotype × location interaction in the first early test. In this test, selecting 20 %, the general predicted genetic gain was G_G = 25.10 %. Identifying progenies with high and stable yield over time and among locations contributes to the efficiency of the genetic breeding program. The relative performance of the progenies varies depending of the age of early selection test.     

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.     

The inheritance of harsh leaves in tetraploid cocksfoot

Research was conducted to study the inheritance of the characteristic ‘dentated leaves’ in the autotetraploid grass species Dactylis glomerata. From segregation ratios of inbred and crossbred populations the following conclusions can be drawn:

1. 1.
   Harshness of leaves is a dominant character. Simplex plants have a dominant phenotype but are less strongly dentated than duplex plants.     
   
   

Development and application of a molecular marker for TMV resistance based on <Emphasis Type="Italic">N</Emphasis> gene in tobacco (<Emphasis Type="Italic">Nicotiana tabacum</Emphasis>)

Tobacco mosaic virus (TMV) caused serious loss in yield and quality of tobacco every year. It is a long-term goal to improve the tobacco resistance against TMV by tobacco breeding. N gene was the firstly reported TMV-resistant gene, which showed resistance against all Tobamoviruses except the Ob stain and belonged to the toll-interleukin-1 receptor/nucleotide-binding site/leucine-rich repeat class of plant resistance (R) genes. At present, N gene had already been widely used in tobacco conventional breeding, but there is rare available molecular maker used in marker-assisted selection of TMV resistance. In this study, we designed a pair of primers that specific amplify N gene fragment based on the sequence of N gene intron III, named N-marker. Then, we identified TMV resistance by two selecting methods, PCR with N-marker and inoculated with the TMV-C strain. Results from the two method showed that (1) 13 varieties among 67 tobacco varieties displayed hypersensitive reaction when inoculated with the TMV-C strain, also contained N gene fragments screened by PCR with N-marker; (2) 105 strains of 200 BC1 strains showed resistance against TMV when inoculated with TMV-C strain, meanwhile, 103 of the 105 strains contained N gene fragment verified by PCR with N-marker. Therefore, the N-marker is reliable for high throughput screening of germplasm resources and tobacco breeding materials in selection of N-mediated TMV resistance. Our study not only developed a molecular marker for tobacco breeding, but also identified new germplasm resources that are resistant to TMV.