Reinventing heterosis phenomenon through deployment of alien introgression lines in rice (Oryza sativa L.)

Introgression Lines (ILs) carrying alien genomic segments in the homozygous state may or may not be able to contribute positively to the phenotype on account of replacement of cultivated genome segment, however, the genetic elite in heterozygous condition can be attributed to the presence of both recipient and donor genome complements. Therefore, overdominance or pseudo‐overdominance effect at the heterozygous loci is anticipated. Set of 318 ILs, carrying several genomic segments from “A” genome donor wild species, were used for developing test hybrids with CMS line PMS17A. Of these, three hybrids observed significant yield advantage (>25%) over recurrent parents and checks. Parental ILs of these hybrids viz., IL326, IL901 and IL951 carried 5.62%, 2.52% introgression from Oryza rufipogon and 6.71% from Oryza nivara, respectively. These ILs were also crossed with their recurrent parent to develop introgression line hybrids (ILHs) to observe the contribution of the alien segment(s), in the homozygous and heterozygous state. The traits studied have higher mean value when genomic segments from wild species were in the heterozygous state as compared to the homozygous state.     

Genetic divergence among a non-restorer collection of sorghum (Sorghum bicolor (L.) Moench) and its relationship with heterosis

Summary A genetic diversity analysis in a collection of 171 non-restorer lines of sorghum (Sorghum bicolor (L.) Moench) using D² technique and canonical variate analysis indicated that considerable variation in grain yield has been added to the collection by the addition of lines derived from random mating populations. The efficiency of D² and canonical variate techniques in distinguishing extremely diverse genotypes was confirmed. However, the two techniques showed weak correspondence in their clusters. The F₁ hybrids of 15 diverse lines exhibited no relationship between heterosis or per se performance of crosses and diversity in their parents. Therefore, traditional plant breeding methods are being advocated.Approved by ICRISAT as Journal Article no. 435.     

Genetic analysis of yield and fruit traits in cantaloupe cultivars

The purpose of this research was to evaluate the combining ability of six local Iranian and one imported cantaloupe cultivar. Heritability of traits was estimated using a half‐diallel mating design. Seven parents and their crosses were evaluated in 2013 and 2014. The greatest general combining ability (GCA) for yield and fruit number was for “Rish‐baba” (0.53 kg/plant and 0.3, respectively). The cultivar “Ananasi” had the highest GCA for fruit weight and soluble solids content (SSC) (0.088 kg and 1.4, respectively). “Ananasi” presented the highest GCA values for fruit firmness, chlorophyll a and b and carotenoid content, as well as the highest total chlorophyll content. The cross Garmak × Rish‐baba showed the highest specific combining ability (SCA) for yield with heterosis value of 99%. High heritability estimates for SSC (0.52), flesh thickness (0.61) and concentration of chlorophyll a (0.7) were obtained. Although there were significant SCAs for yield, the parents are suggested to be improved prior to hybrid development. The parent “Ananasi” appears to be a suitable donor in breeding programmes.     

Using yield quantitative trait locus targeted SSR markers to study the relationship between genetic distance and yield heterosis in upland cotton (Gossypium hirsutum)

The objective of this study was to examine the relationship between heterosis and genetic distance in upland cotton (Gossypium hirsutum L.). Heterosis in the different environments was evaluated and the relationship between heterosis and genetic distance (GD) was determined based on SSR markers for yield quantitative trait loci (QTL). Yields of seed cotton and lint showed a linear relationship with mid‐parent heterosis (MPH) and better‐parent heterosis (BPH). The variation in heterosis for other traits and their correlation with GD may be due to environmental factors or the effort of QTLs tested in the present study may vary in different environments. The present findings provide a foundation for heterotic grouping of parental lines and breeding of new cotton hybrids with improved seed cotton yield. This study calls for more research with stable QTLs as well as advance molecular marker techniques may be used in predicting yield heterosis in a more precise and reliable manner.     

Genetic diversity and population structure of the selected core set in Amaranthus using SSR markers

The genus Amaranthus has gained much attention, particularly for its high economic and nutritional value. It is a genus of taxonomic complexity with many interspecific hybrids. For effective conservation and management of the germplasm collected, the development of a core set of accessions is especially important. A core set of 63 accessions was successfully developed from an entire collection of 634 accessions using the powercore 1.0. Among the tested methods for developing the core set – the advanced M strategy using the modified heuristic method (HCC), randomly chosen collections and stratified random collections – HCC was found to be best, with 100% coverage of alleles and minimum redundancy. Allele frequency distribution of the core set developed with HCC was highly correlated with that of entire collections (r = 0.91). Model‐based structure analysis revealed the presence of three subpopulations and 11 admixtures in the selected core set, which is basically consistent with clustering based on the genetic distance. The results from this study will provide effective information for future germplasm conservation and improvement programmes in Amaranthus.     

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.     

Development of broad‐spectrum bacterial blight resistance into thermo‐sensitive genic male sterile lines

Two‐line hybrid rice technology is an effective way to increase rice production and improve rice quality. In this study, three bacterial blight (BB) resistance genes, Xa7, Xa21 and Xa23, were introgressed separately into C815S, a popular thermo‐sensitive genic male sterile (TGMS) line to develop five BB‐resistant lines (Hua1005S, Hua1002S, Hua1009S, Hua1006S and Hua1001S) to be resistant against seven races of Xanthomonas oryzae pv. oryzae (Xoo). The two‐line hybrids with heterozygous Xa23 were resistant against seven Xoo strains. But, the hybrids with heterozygous loci for both Xa7 and Xa21 were only resistant against three Xoo strains and were moderately susceptible to the other four strains indicating the role of modifiers influencing the poor expression of dominant BB resistance genes under heterozygous state. Among them, Hua1006S was found to be a promising TGMS line with its higher degree of disease resistance level on account of broad‐spectrum resistance gene Xa23 besides possessing better plant type and rice grain quality features.     

Integration of AFLPs,SSRs and SNPs markers into a new genetic map of industrial chicory (Cichorium intybus L. var. sativum)

A chicory genetic map of 1208 cM has been created using 247 F₂ plants and 237 markers (170 AFLP, 28 SSR, 27 EST‐SNP and 12 EST‐SSR). This map covers 84% of the chicory genome. The chicory‐genic‐markers‐associated sequences were used to find potential orthologs in mapped lettuce ESTs from the Compositae Genome Project Database. Twenty‐seven putative orthologous pairs were retained, pinpointing seven putative blocks of synteny that covered 11% of the chicory genome and 13% of the lettuce genome, opening new perspectives for the analysis of these two species.     

Gene effects of Cicer reticulatum on qualitative and quantitative traits in the cultivated chickpea

The gene effects of Cicer reticulatum on both double‐podding as qualitative traits and yield criteria as quantitative traits in interspecific hybridization with cultivated chickpea (Cicer arietinum) have not yet been elucidated, despite the easy acquisition of hybrid progeny between two species. This study sought to answer three questions concerning qualitative and quantitative traits in reciprocal crosses between C. arietinum and C. reticulatum. (i) Is there a similarity in the gene effects of flower colour, pigmentation and double‐podded traits in reciprocal interspecific crosses? (ii) What are the expressivity and penetrance of the double‐podded trait in interspecific crosses? (iii) Which heterosis predicts the occurrence and the extent of transgressive variation? The materials for this study were F₁, F₂ and F₃ progeny derived from a reciprocal cross between C. arietinum and C. reticulatum. As qualitative traits, purple flower colour, pigmentation and single‐podded traits in C. reticulatum were governed by a dominant single gene. Purple flower colour and pigmentation were detected to be linked traits as all progeny had the same phenotypes. As quantitative traits, yield criteria in progeny which were double‐podded had higher values than the single‐podded counterparts. Expressivity and penetrance of the double‐podding trait were superior in progeny derived from C. reticulatum × C. arietinum. The results showed that fruitful heterosis was more useful than residual heterosis in F₃ as residual heterosis was mostly negative and fruitful heterosis was suggested in self‐pollinated species such as chickpea that lacks inbreeding depression. Interspecific transgression was significant with respect to chickpea improvement because it represented a potential source of novel genetic variation.     

Use of barley seed vigour to discriminate drought and cold tolerance in crop years with high seed vigour and low trait variation

Seed vigour is a precondition for early and homogenous field emergence of barley, in addition to effective malting. This study aimed to assess the selection of barley varieties by using seed vigour as the indicator. Seed vigour of barley (quantified as the germination percentage) was evaluated under drought (?0.2 MPa) and temperature stress (10°C). At two locations over a 3‐year period, 1 population of 133 Derkado × B83‐12/21/5 doubled haploid (DH) lines (and parents) was evaluated for seed vigour, of which 108 DH lines were assessed for three malting parameters. The relatively high values of vigour during the 3‐year period (overall average 94–95%) probably impeded high variations in genetic potential. A total of 27 DH lines of the 133 evaluated showed transgression for vigour (up to 98%) in comparison with the parents (Derkado: 96%; B83: 92%). In conclusion, caution should be applied when selecting for seed vigour, even in good crop years with high levels of seed vigour and low trait variations. Such selection might improve vigour, particularly in crop years with unsuitable weather conditions.     

Identification and gene cloning of a male‐sterile mutant Oswbc11 in rice

Commercial application of nuclear genetic male sterility has been improved recently by a novel technique, Seed Production Technology (SPT), which incorporates transgenic maintainer lines capable of propagating non‐transgenic nuclear male‐sterile lines for use as female parents in hybrid production. Here, we identified a rice nuclear male‐sterile mutant, Oswbc11, with abnormal pollen development and lipid transport. We finely mapped the Oswbc11 gene into a 12.5‐kb region on chromosome 10 and found one candidate gene, which had a base substitution (C to T) resulting in a premature stop codon and was functionally confirmed by CRISPR/Cas9 technology. Gene OsWBC11 encodes a sub‐family member of adenosine triphosphate‐binding cassette transporter, which participates in the active transport of a wide range of molecules across membranes. Moreover, the agronomic traits of Oswbc11 mutants showed no significant differences compared to the wild‐type control except for the seed setting rate. These results indicated that Oswbc11 gene could be used in rice hybrid breeding as a recessive nuclear male‐sterile gene combined with CRISPR/Cas9 and the SPT technology and applied in different rice varieties.     

Mechanisms and diversity of resistance to sorghum shoot fly,Atherigona soccata

Sorghum shoot fly, Atherigona soccata, is one of the important pests of postrainy season sorghums. Of the 90 sorghum genotypes evaluated for resistance to this pest, RHRB 12, ICSV 713, 25026, 93046 and 25027, IS 33844‐5, Giddi Maldandi and RVRT 3 exhibited resistance in postrainy season, while ICSB 463, Phule Anuradha, RHRB 19, Parbhani Moti, ICSV 705, PS 35805, IS 5480, 5622, 17726, 18368 and 34722, RVRT 1, ICSR 93031 and Dagidi Solapur showed resistance in rainy season, suggesting season‐specific expression of resistance to A. soccata. ICSB 461, ICSB 463, Phule Yasodha, M 35‐1, ICSV 700, 711, 25010, 25019 and 93089, IS 18662, Phule Vasudha, IS 18551 and 33844‐5 and Barsizoot had fewer deadhearts than plants with eggs across seasons, suggesting antibiosis as one of the resistance mechanism. Five genotypes exhibited resistance with high grain yield across seasons. Correlation, path and stepwise regression analyses indicated that leaf glossiness, seedling vigour, trichome density, oviposition and leaf sheath pigmentation were associated with the expression of resistance/susceptibility to shoot fly, and these can be used as marker traits to select and develop shoot fly‐resistant sorghums.     

Cross‐genera amplification of informative microsatellite markers from common bean and scarlet runner bean for assessment of genetic diversity in mungbean (Vigna radiata)

Mungbean (V. radiata) is an important Asiatic legume supplying inexpensive protein to a vast majority of vegetarian masses. To increase markers repertoire in mungbean, a study was conducted to analyse 384 microsatellite markers derived from common bean, scarlet runner bean and adzuki bean for their transferability and polymorphism. The results showed that 87 (24.71%) primer pairs could amplify DNA loci of 20 mungbean genotypes including one accession of V. trilobata, while 52 showed reliable banding and polymorphism. These showed different degrees of variability at each locus producing 250 alleles with the number of alleles varying from 2 to 9. The major allele frequency varied from 0.17 to 0.95, while the polymorphic information content of SSRs ranged between 0.09 and 0.86 with an average of 0.60 ± 0.16. UPGMA revealed three major clusters accommodating ~95% of the accessions while one accession of V. trilobata (‘NSB‐007’) did not group with any other genotype describing the discriminating power of informative microsatellites. This study identified a set of useful microsatellite markers to accelerate the genetic studies and breeding programme of mungbean.     

Quantification of critical factors affecting fitness of the sugary1 mutant in maize

Fitness of sugary1 (su1) is affected by some critical traits that depend on the genotypes and environments, while their effects have not been quantified with convincing statistical methods. The objective of this work was to identify and quantify the critical factors of su1 fitness with different genotypes and environments. We used two pairs of field corn inbreds that differentially affected su1 viability to develop F₁, F₂, BC₁ and BC₂. After selfing, Su1 and su1 kernels were evaluated under controlled environmental conditions and in field trials. Multiple regressions showed that dry weight of juvenile plant was affected by early vigour (plant size, colour and health) and emergence in cold conditions; ear weight by plant appearance, number of plants and chlorophyll content; number of ears by plant appearance, number of plants, chlorophyll content and female flowering; and kernel weight by ear weight, number of plants, row number and ear length. The main critical factors for su1 fitness were early vigour and emergence under cold conditions at initial stages, while several adult traits were related with final fitness.     

Genetic diversity of tropical maize inbred lines combining resistance to Striga hermonthica with drought tolerance using SNP markers

Striga hermonthica and drought are the major stresses limiting maize yields in sub‐Saharan Africa. The search for diverse maize lines’ tolerance to drought and resistance to S. hermonthica (DTSTHR) is very crucial for yield improvement in areas affected by the two stresses. Understanding the genetic diversity among the lines is important to develop cultivars resistant to S. hermonthica and tolerant to drought. The lines were developed from biparental crosses of drought‐tolerant and Striga‐resistant lines. A total of 128 DTSTHR maize lines were characterized using single‐nucleotide polymorphism (SNP) markers. Results of the cluster analysis based on 3297 SNP markers showed four distinct groups consistent with the pedigrees of the lines. Furthermore, model‐based analysis also formed the same groups of the DTSTHR lines. Integrating the pedigree information with combining ability and the SNP analyses may provide defined heterotic groups for maize improvement work in West and Central Africa. These results also help breeders to utilize DTSTHR lines present at IITA for developing biparental crosses without disrupting the heterotic groups they have established in their breeding programmes.     

Germplasm enhancement of maize: a look into haploid induction and chromosomal doubling of haploids from temperate‐adapted tropical sources

The allelic diversity (AD) project of the Germplasm Enhancement of Maize (GEM) programme utilized the double haploid (DH) breeding method to expedite development and release of lines derived from 300 exotic maize races. Using 18 races in this study, differential effects on haploid induction rates (HIRs) and doubling rates (DRs) by the recurrent parents PHB47 and PHZ51, the elevation that the race is traditionally grown at, and by the race itself were addressed in this study. Races from the AD project were grouped by elevation of their origin, high, middle or low altitude. Six races per elevation were randomly selected and backcrossed using both recurrent parents to generate 36 populations. Ten replications were randomized in a complete randomized design for two growing seasons. The recurrent parent effect was significant, with PHB47 having a higher HIR than PHZ51. Effect of elevation was significant with higher HIR associated with low‐elevation origin, and race also proved to be significant. Effects of elevation, recurrent parent and race were not significant for DR.     

Introgression of productivity and other desirable traits from ricebean (Vigna umbellata) into black gram (Vigna mungo)

Crosses were performed to introgress genes for productivity and other desirable traits from ricebean (Vigna umbellata) into black gram (Vigna mungo). Crossability was very poor in black gram × ricebean crosses, and only two to nine true hybrid plants were obtained. Plant fertility was very poor in initial generations, but was improved gradually from F₂ onwards. Twenty‐four uniform progenies, bulked in F₇, were evaluated for yield potential. The percentage increase/decrease in yield ranged from ?35.48 to 50.31 over the check cultivar (‘Mash338’, female parent). All the progenies were found resistant to Mungbean yellow mosaic virus, Cercospora leaf spot and Bacterial leaf spot diseases. Overall, it was found that desirable traits such as high pod number, seed weight, productivity and resistance to diseases have been introgressed successfully into black gram from ricebean. A derivative line, KUG114, recorded yield superiority of 39.45% over the check cultivar ‘Mash338’ on the average of 14 multilocation research trials. It was released under the name ‘Mash114’ for cultivation in the Punjab state.     

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.     

New insights into genotypic thermodependency of cytoplasmic male sterility for hybrid barley breeding

The cytoplasmic male sterility (CMS) system msm1 in barley is known to be thermosensitive, sometimes resulting in spontaneous fertility restoration in the absence of the corresponding restorer gene Rfm1. Here, we investigated genotypic differences concerning temperature sensitivity and the plant developmental stage at which elevated temperature induces spontaneous fertility restoration in three CMS mother lines. While one line stayed completely male sterile, a significantly higher fertility was observed in two lines after treatment from growth stage DC 41 until maturation. Microscopic analysis revealed that sterile anthers contained neither intact pollen, nor remains of aborted pollen grains, whereas pollen was visible in anthers of potentially fertile plants. We conclude that the barley CMS system affects anther and pollen development prior to meiosis. Elevated temperature during heading and flowering can lead to a spontaneous fertility restoration by reactivating pollen growth. Nevertheless, genotypic variation exists enabling the selection for stable CMS mother lines and the development of F₁ hybrids with high hybridity. As spontaneous fertility restoration due to environmental effects is difficult to phenotype, further investigations will focus on the development of molecular markers for marker‐assisted selection.