Improving seed yield in red clover through marker assisted parentage analysis

Red clover (Trifolium pratense L.) is an important perennial forage crop in Europe. Unfortunately, seed production of modern cultivars is often unsatisfactory and breeding progress for higher seed yield is slow. We evaluated whether marker assisted parentage analysis could identify progeny plants with two high seed-yielding parents in a diploid selection trial. Furthermore, we studied if breeding for high seed yield could be speeded up by selecting progeny plants with two high seed-yielding parents, compared to traditional selection on the mother plant only. In this study, 111 genotypes with excellent vegetative traits from a first cycle selection trial were allowed to pollinate each other in isolation. After seed harvest, ten high seed-yielding plants were identified and their seeds were used to grow ten half-sib progeny populations, with 1,121 plants in total. Two multiplex primer sets targeting 18 SSR loci were designed and used to fingerprint parental and progeny plants. Parentage was reliably determined for 1,083 progeny plants: 135 plants were the result of a cross between two high seed-yielding parents. In a 2-year seed yield trial, the seed yield of these 135 progeny plants was compared to that of a control group of 216 progeny plants from the same ten high seed-yielding mother plants but with no selection on the male contribution, as is current practice. Compared to the control group, progeny plants with two high seed-yielding parents had significantly higher seed yields, 23.0 and 75.9 % higher in 2012 and 2013 respectively, and a significantly higher thousand seed weight, 6.6 and 5.7 % higher in 2012 and 2013 respectively. Seed yield was strongly correlated with flower abundance (r = 0.643) and plant volume (r = 0.593 in 2012 and r = 0.509 in 2013) and negatively correlated with susceptibility to mildew (r = ?0.145). We conclude that breeding programs aiming at increasing seed yield in diploid red clover cultivars would strongly benefit from the integration of marker assisted parentage analysis to identify those progeny plants that are the result of a cross between two high seed-yielding plants. This goal cannot be achieved with traditional family selection where only the seed yield of the mother plant is known.     

Influence of flower and flowering characteristics on seed yield in diploid and tetraploid red clover

Tetraploid red clover (Trifolium pratense L.) often produces insufficient seed to be economically interesting. Numerous studies have identified poor pollination due to long corolla tubes as its cause, but other studies disagree. Therefore, we investigated seed yield, corolla tube length and flowering traits in 244 plants from five diploid and five tetraploid cultivars during 2 years. Tetraploids produced fewer seeds, fewer flower heads and fewer seeds per head, but an equal number of flowers per head when compared to diploids. Although corolla tubes were longer in tetraploid than in diploid red clover (P < 0.001), no correlation between corolla tube length and seed yield was detected. Therefore, the corolla tube length is likely neither the main nor only cause of low seed yield in tetraploid red clover. Instead, three putative causes for low seed yield were identified: tetraploids produced less inflorescences per plant, possessed a lower degree of determinacy and had markedly less seeds per head when compared to diploids. Possible causes for such differences include lower pollen viability and higher rates of embryo abortion.     

Breeding cowpea for resistance to Striga gesnerioides in the Nigerian dry savannas using marker‐assisted selection

Historically, conventional breeding has been the primary strategy used to develop a number of Striga‐resistant varieties currently grown in the Sahel of Western Africa. In this study, we have successfully developed and applied a marker‐assisted selection strategy that employs a single backcross programme to introgress Striga resistance into farmer preferred varieties of cowpea for the Nigeria savannas. In this strategy, we have introduced the Striga resistance gene from the donor parent IT97K‐499‐35 into an elite farmer preferred cowpea cultivar ‘Borno Brown’. The selected 47 BC₁F₂ populations confirmed the recombinants with desirable progeny having Striga resistance gene(s). The 28 lines selected in the BC₁F_2:4 generation with large seed size, brown seed coat colour and carrying marker alleles were evaluated in the field for resistance to Striga resistance. This led to the selection of a number of desirable improved lines that were immune to Striga having local genetic background with higher yield than those of their parents and standard varieties.     

Validation of molecular markers for pathogen resistance in potato

DNA markers have a large potential to improve efficiency and precision of conventional plant breeding programmes based on marker‐assisted selection (MAS). In our study, we have evaluated the predictive abilities of the SCAR marker RYSC3 and the CAPS marker GP122₅₆₄ with regard to the PVY resistance genes Ry_adg and Ry_sto, respectively, and of marker TG689 linked to H1 conferring resistance to Globodera rostochiensis and marker HC associated with high levels of G. pallida resistance. The evaluations were made in 28 cultivars and accessions and in 219 progeny genotypes descending from ten different crosses. We observed in all evaluated cultivars and accessions the expected marker patterns according to their phenotypic classification into resistant and susceptible genotypes. However, in part considerable discrepancies were observed when analysing progeny of controlled crosses involving these resistance sources, particularly with respect to H1. Based on these results, practical aspects for the efficient implementation of marker‐assisted selection are discussed, which consider the genetic origin of the material, costs aspects and methodology applied.     

Validation of male sex‐specific UBC‐8071200 ISSR marker and its conversion into sequence tagged sites marker in Jojoba: a high precision oil yielding dioecious shrub

There is a recent surge in the marker‐assisted selection of desired sex type among economically important dioecious crops. Simmondsia chinensis (Jojoba), a dioecious crop is of immense agricultural importance where only the female plants are preferred for commerce. DNA fingerprinting technology, ISSR analysis along with bulk segregant analysis (BSA), has been carried out on a diverse set of 17‐ to18‐year‐old mature male and female plants of Jojoba to validate a male sex‐specific ISSR marker, UBC‐807₁₂₀₀ on larger population that comprises 330 female and 255 male plants of Jojoba. This male sex‐specific DNA fragment of ~1200 bp was cloned and sequenced. The sequence was found to be 1120 bp in length and based on the sequence information, a pair of sequence tagged sites primers was developed that amplified a single ~800 bp band, consistently only in all the male populations while no amplification was seen in their female counterparts. The marker was named as Jojoba Male Sex Marker which was further validated on 330 female plants from 22 genotypes and 255 male plants from 17 genotypes.     

Genotype selection for physiological responses of drought tolerance using molecular markers in polycross hybrids of orchardgrass

The present study aimed to assess the effect of contrasting levels of molecular and phenotypic diversity among polycross parents of orchardgrass on the performance of synthetic progeny with respect to physiological responses and drought tolerance. Four polycross groups each composed of six parental plants were evaluated under normal irrigation and drought stress conditions. A number of 923 inter simple sequence repeats and sequence related amplified polymorphism markers and several phenotypic traits were used to select contrasting levels of diversity (high and low) in parental genotypes. Highly significant correlation was observed between molecular distance and progeny performances at both normal irrigation and drought stress conditions. High molecular diversity among polycross parents led to a significant yield advantage of first generation progeny with averages of 34.40% for normal irrigation and 48.10% for drought stress conditions. Also crosses between genetically distant parents produced progeny with considerable drought tolerance and yield stability. Positive associations between phenotypic distance of parents and progeny performance were found for most physiological traits at both moisture regimes but phenotypic distances had weak association with forage yield, stress tolerance index and yield stability of progeny. Significant associations between drought tolerance index and some physiological traits confirmed the importance of these traits in conferring drought tolerance of orchardgrass. Our results underscore the effectiveness of marker‐assisted polycross breeding to improve drought tolerance and yield stability through physiological traits in orchardgrass.     

The potential of genomic‐assisted breeding to improve Fusarium head blight resistance in winter durum wheat

Durum wheat is the most important tetraploid wheat mainly used for semolina and pasta production, but is notorious for its high susceptibility to Fusarium head blight (FHB). Our objectives were to identify and characterize quantitative trait loci (QTL) in winter durum and to evaluate the potential of genomic approaches for the improvement of FHB resistance. Here, we employed an international panel of 170 winter and 14 spring durum lines, phenotyped for Fusarium culmorum resistance at five environments. Heading date, plant height and mean FHB severity showed significant genotypic variation with high heritabilities and FHB resistance was negatively correlated with both heading date and plant height. The dwarfing gene Rht‐B1 significantly affected FHB resistance and the genome‐wide association scan identified eight additional QTL affecting FHB resistance, explaining between 1% and 14% of the genotypic variation. A genome‐wide prediction approach yielded only a slightly improved predictive ability compared to marker‐assisted selection based on the four strongest QTL. In conclusion, FHB resistance in durum wheat is a highly quantitative trait and in breeding programmes may best be tackled by classical high‐throughput recurrent phenotypic selection that can be assisted by genomic prediction if marker profiles are available.     

Breeding for the improvement of the ideal plant type of sesame

The objective of this study was to improve the ideal type of sesame, by performing pedigree selection applied to segregating generations of crosses of genotypes with contrasting characters. In the segregating F₂ population, the progeny were classified into eight types according to the combinations of carpel number per capsule, capsule number per axil and branching habit. Progeny of individual F₂ plants including a particular type were advanced to the F₆ generation. It was possible to improve the lines with eight types at the end of the selection process. Some types, especially bicarpels, monocapsule, branch (BMB) and bicarpels, tricapsules, branch (BTB), were considered as ideal plant types in breeding for high‐yielding varieties. While the low‐yielding type quadricarpels, tricapsules, non‐branch (QTN) was the highest in oil content (49.3%), the high‐yielding type BMB was the lowest (43.2%), Although the QTN‐type had the lowest content of oleic acid (41.3%) and the highest content of linoleic acid (43.1 %), the bicarpels, monocapsule, non‐branch (BMN) type had the highest content of oleic acid (48.4%) and the lowest content of linoleic acid (36.6%), Total tocopherol varied between 175.6 and 368.9 mg/kg in the seed oil of the sesame types. The best high‐yielding type BMB was one of the types containing less tocopherol.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.     

A maximin–minimax approach for classifying soybean genotypes for drought tolerance based on yield potential and loss

Screening for drought in soybean is often a bottleneck in plant breeding programmes. Sixteen genotypes were evaluated for drought tolerance during 2012, 2013 and 2014. The experiment was conducted in a split‐plot design, and the main plots consisted of irrigated and water stress treatments, and subplots consisted of 16 genotypes. The average seed yield was highest in 2012 (1708 kg/ha), followed by 2014 (1364 kg/ha) while very low yields (958 kg/ha) were observed during 2013. The per cent reduction in average soybean yield under water stress conditions was maximum (43%) during 2014 followed by 2012 (40%) and 2013 (31%), respectively. The average yields of soybean genotypes also differed significantly, which ranged from 892 (NRC 12) to 2008 kg/ha (JS 97‐52). The maximin–minimax approach was used to classify these genotypes, and only, one genotype was identified as drought resistant and high yielding (EC 538828), three as tolerant and high yielding (JS 97‐52, EC 456548 and EC 602288) and none as low yielding and resistant, while the remaining 12 genotypes were found to be low yielding and susceptible to drought.     

Evaluation of Self and Polycross Progeny Testing in Birdsfoot Trefoil (Lotus corniculatus L.) for Forage and Seed Yield

Self and cross fertility, forage and seed yield of parents, self (Sl), and polycross (PX) progenies were measured in a selected and an unselected population of birdsfoot trefoil (Lotus corniculatus L.), Self fertility was significantly less than cross fertility in both populations. In a field planting S1 progenies had lower forage yield in 1979 and 1980 and seed yield (relative to the parents) was less in the selected population than the unselected in 1979. All correlation coefficients between years and progenies were non-significant for forage yield bur the parents-poly cross progeny correlation was significant for seed yield in the selected population. Percentage survival of plants after cutting in 1980 was higher in the selected population, and the parents and PX progenies survived better than S1 progenies in both populations. The better performance of the selected population may be due, in pan, to higher frequency of favorable genes resulting from four cycles of recurrent selection, S1 progeny testing does not appear to be worth while in birdsfoot trefoil because of low self fertility and the reduced vigour of the progeny.     

Genetic and environmental effects on the occurrence of speltoids in winter wheat cultivars

The occurrence of speltoid off‐types during seed multiplication is one of the major causes for rejection of a wheat cultivar candidate due to phenotypic inhomogeneity. These aberrant plants express an atypical spear‐shaped spike with tenacious glumes. To analyse the frequency of speltoids under field conditions, field trials were conducted at three locations and two sowing times over 2 years based on speltoid off‐type spikes derived from 14 different wheat genotypes. One hundred single ear progeny were developed from the normal and speltoid progeny plants in 2007. A mean frequency of 21.1% and 36.6% speltoid off‐types in plots from normal and speltoid lines was observed, respectively. Plots sown late in the season displayed on average 5.3% less speltoid off‐types, in particular when both sowing times were far apart. Field trials from 2010 revealed 7.9% more aberrant plants compared with 2011. The percentage of speltoids within the field plots ranged from 0.2% to 83.7%, which indicates a large effect of the respective genotype. Finally, strategies to reduce the number of speltoid off‐types are discussed.     

Response of cotton genotypes to water and heat stress: from field to genes

Cotton is a crop of tropical and subtropical regions but the seed cotton yield is highly influenced by abiotic stresses like drought and heat. Response of cotton genome to abiotic stresses is highly complex and involve many genes. A comprehensive study, involving cotton genotypes developed through conventional and synthetic tetraploid method, was designed to (i) study the introgression of heat and water stress tolerance by using wild relatives (ii) evaluate genetic markers for marker assisted selection against water and heat stress. Two separate experiments for water and heat stress tolerance with a common control were established. Treatments in each experiment include a control and a stress treatment. Heat stress was applied by sowing crop two month earlier than the control treatment, whereas water stress was imposed by withholding alternate irrigation. Analyses of variance depicted highly significant (P ≤ 0.01) effect of genotypes and both stresses on boll retention, boll weight and seed cotton yield. Interaction of genotypes with stress in both experiments was also highly significant (P ≤ 0.01). Genotypes derived from interspecific crosses performed consistently in stress conditions compared to control which prove it a reliable method to introgress stress related genes from wild parents. Four genes reported for water stress tolerance and five genes reported for heat stress tolerance were evaluated by field results for efficient marker assisted selection (MAS). Results verified drought stress genes but heat stress genes could not explain genetic variability caused by heat stress. It is concluded from the results that separate genes may be responsible for heat stress tolerance for vegetative and reproductive stages, therefore, selection criteria should include both the traits.     

Farmer participatory evaluation confirms higher grain yields in spring wheat using a selection index for spot blotch resistance, maturity and kernel weight

Wheat (Triticum aestivum L.) cultivars for the warm regions of South Asia must produce high yields and possess resistance to spot blotch (Cochliobolus sativus), early maturity and high kernel weight. A study was conducted to determine the effectiveness of selecting for high grain yield based on a selection index for spot blotch resistance, maturity and kernel weight in four wheat crosses involving a susceptible cultivar and resistant genotypes. Initial selection of 40 progeny lines in each cross had been made using a selection index based on disease severity, days to heading and kernel weight as reported by Sharma and Duveiller [{Crop Sci 43 (2003) 2031}]. The five highest grain-yielding progeny lines from among the 40 lines in each cross, their parents and five popular commercial cultivars were evaluated in field trials at two sites in Nepal in the 2002 and 2003 wheat seasons. Multiple spot blotch assessments were made to determine the area under disease progress curve (AUDPC). Grain yield, thousand-kernel weight (TKW), days to heading and plant height were examined. The wheat genotypes in the farmer's field were also ranked on the basis of cultivar preference criteria by the local farmers. The 20 progeny lines always showed a higher (+11 to +125%) grain yield and heavier (+10 to +44%) kernels than their parents and a lower (−83 to −89%) AUDPC than the susceptible parent. The progeny lines showed 98–100% grain yield, 97–100% TKW and 66–78% AUDPC compared to the highest grain-yielding commercial cultivar. Based on the farmers' preference criteria for a desirable wheat genotype, the best progeny lines ranked from 3rd to 5th, whereas the two commercial cultivars ranked 1st (Gautam) and 2nd (BL 1473). Results indicated that selection was effective in combining adaptation genes present in a local cultivar with some level of tolerance to spot blotch and resistance genes from exotic genotypes, which translated into improved agronomic performance and disease resistance. The selection index and farmer participatory approach used in this study could serve as a guideline in breeding efforts targeted for high yielding genotypes for wheat-growing conditions in South Asia where spot blotch is a serious biotic constraint to yield.     

Effect of plant density on selection for seed yield in two population types of Phaseolus vulgaris L.

Summary Pedigree selection for seed yield, using early generation yield tests, was practiced from the F₂ to F₇ in two populations of common bean (Phaseolus vulgaris L.) in three plant densities: 66, 133, and 266 thousand plants ha^-1 at CIAT-Palmira, Colombia. The six highest yielding lines selected from each plant-density, along with 13 parents, were evaluated in a 7×7 lattice design with three replications at the three densities utilized for selection, and at 399,000 plants ha^-1 in 1988 and 1989.Based on the mean performance of selected lines and the mean of the parents, selection for seed yield was effective in all densities in both populations. However, none of the lines selected from the population within the race Mesoamerica (TC 4673) significantly outyielded their best parent under any plant density. The highest yielding lines selected from the interracial population (TR 4635) outyielded their best parent irrespective of the plant-density used for selection. The highest yielding line originated from the highest density used for selection. Low density was neither good for selection nor for evaluation and identification of high-yielding cultivars of common bean. There was no significant difference between the mean yield of lines selected at the intermediate and high population densities. The effects of plant density, year, and their interactions were significant for seed yield.     

S‐locus diversity and cross‐compatibility of wild Prunus avium for timber breeding

Prunus avium is primarily cultivated for its fruit, sweet cherries. However, it is also used to produce high‐quality timber. In a P. avium seed orchard, gametophytic self‐incompatibility is a restriction for free pollen flow and should be considered when establishing basic forest materials. In this study, S‐locus diversity and cross‐incompatibility of wild cherry individuals in clonal banks established for breeding for timber production were investigated. Wild cherry trees (140) with outstanding forest growth habit, collected in northern Spain, grafted and planted in two clonal banks, were genotyped at the S‐locus. The self‐incompatibility S‐locus genes, S‐RNase and SFB, were analysed by PCR. Twenty‐two S‐haplotypes, resulting in 72 different S‐genotypes, were identified. The genotypes were grouped into 33 incompatibility groups and 39 unique genotypes. This initial S‐locus analysis revealed large genetic diversity of wild cherry trees from the Spanish northern deciduous forest, and provides useful information for seed orchard design. Wild P. avium displays significantly more genetic diversity than what is detected in local cultivars, revealing a narrowing of genetic diversity during local domestication.     

Seed Shattering of Cañahua (Chenopodium pallidicaule Aellen)

Cañahua (Chenopodium pallidicaule Aellen) is a semi‐domesticated relative of quinoa (Chenopodium quinoa Willd.) with high nutritious quality. It is tolerant to frost, drought, saline soils and pests. One seed yield limitation is seed loss during the maturity stages. Two greenhouse experiments in Denmark and field experiments in Bolivia were carried out to determine seed shattering in landraces and cultivars with different growth habits. 15–21 % of the seed shattering in the fields took place whilst the plants still were flowering and 25–35 % during physiological maturity. Seed shattering varied between locations on the Bolivian Altiplano. Cañahua types with the semi‐prostrate growth (‘lasta’) had the highest seed shattering rate in the greenhouse experiments. The Umacutama landrace had lower seed shattering (1 %) than the cultivar Kullaca (7.2 %) both of the ‘lasta’ type. Under field conditions, the cultivar Illimani with the erect growth (‘saihua’) had the highest seed shattering rate (6.4–33.7 %) at both locations and at four different sowing dates. The Umacutama had the lowest rate (0.5–1.5 %). There were no significant differences between plants of the ‘lasta’ and the ‘saihua’ types. The landrace had significantly less seed loss than the cultivars. However, in the greenhouse, the landrace yield was approximately 25 % lower than the yields of the cultivars. In general, cañahua cultivars had higher yield compared to landraces, but also a higher seed shattering rate. Landraces may be used in breeding programmes to develop high‐yielding cultivars with reduced seed shattering.     

Mapping of male sterility gene ms10 in chilli pepper (Capsicum annuum L.)

Most of the hybrid seed in chilli are produced manually, but the use of male sterility (MS) can reduce the cost of hybrid seed production. MS‐12, a nuclear male‐sterile (NMS) line developed at Punjab Agricultural University, Ludhiana (India), has been utilized to develop commercial F₁ hybrids. A recessive gene, designated as ms10, governs MS in MS‐12. Due to recessive gene control, development of new NMS lines incorporating ms10 gene is tedious and time‐consuming. We identified SSR markers AVRDC‐PP12 and AVRDC_MD997* linked to the ms10 gene. A total of 558 primer pairs were screened following bulked segregant analysis (BSA). Linkage analysis in 210 F₂ plants indicated that the two SSR markers were linked to the ms10 gene and the marker AVRDC‐PP12 was closest to the gene at 7.2 cM distance. The marker was mapped to chromosome 1 at genome position 175 694 513 to 175 694 644. Until more closely linked markers are developed, the marker AVRDC‐PP12 would facilitate transfer of ms10 gene through marker‐assisted selection (MAS). Fine mapping would lead to cloning of the ms10 gene.     

Identification and marker‐assisted introgression of QTL conferring resistance to bacterial leaf blight in cowpea (Vigna unguiculata (L.) Walp.)

Bacterial leaf blight (BLB), caused by Xanthomonas axonopodis pv. vignicola (Xav), is widespread in major cowpea [Vigna unguiculata (L.) Walp.] growing regions of the world. Considering the resource poor nature of cowpea farmers, development and introduction of cultivars resistant to the disease is the best option. Identification of DNA markers and marker‐assisted selection will increase precision of breeding for resistance to diseases like bacterial leaf blight. Hence, an attempt was made to detect QTL for resistance to BLB using 194 F_2 : 3 progeny derived from the cross ‘C‐152’ (susceptible parent) × ‘V‐16’ (resistant parent). These progeny were screened for resistance to bacterial blight by the leaf inoculation method. Platykurtic distribution of per cent disease index scores indicated quantitative inheritance of resistance to bacterial leaf blight. A genetic map with 96 markers (79 SSR and 17 CISP) constructed from the 194 F₂ individuals was used to perform QTL analysis. Out of three major QTL identified, one was on LG 8 (qtlblb‐1) and two on LG 11 (qtlblb‐2 and qtlblb‐3). The PCR product generated by the primer VuMt337 encoded for RIN2‐like mRNA that positively regulate RPM1‐ and RPS2‐dependent hypersensitive response. The QTL qtlblb‐1 explained 30.58% phenotypic variation followed by qtlblb‐2 and qtlblb‐3 with 10.77% and 10.63%, respectively. The major QTL region on LG 8 was introgressed from cultivar V‐16 into the bacterial leaf blight susceptible variety C‐152 through marker‐assisted backcrossing (MABC).     

Genome mapping and molecular markers identification for yield,yield component and fibre quality traits in tetraploid cotton

The identification of quantitative trait loci (QTL) across different environments is a prerequisite for marker‐assisted selection (MAS) in crop improvement programmes. CottonSNP63k Illumina infinium array was used for genotyping 178 inter‐specific recombinant inbred lines and the parents, and identified 1,667 homozygous polymorphic markers between the parents. Of these, 1,430 markers were used for the construction of linkage map after removing 237 redundant markers. The genetic map spans a total genetic length of 3,149.8 cM with an average marker interval size of 2.2 cM. The phenotypic data from five environments were analysed separately using inclusive composite interval mapping which identified a total of 56 QTL explaining phenotypic variances (PVE) in the range of 8.18%–28.91%. There were 11 and 24 major QTL found for fibre quality and yield components, respectively. A total of 64 QTL were identified through Multi‐Environment Trials analysis, of which 34 recorded QTL × Environment interactions.