Comparative mapping of Raphanus sativus genome using Brassica markers and quantitative trait loci analysis for the Fusarium wilt resistance trait

Fusarium wilt (FW), caused by the soil-borne fungal pathogen Fusarium oxysporum is a serious disease in cruciferous plants, including the radish (Raphanus sativus). To identify quantitative trait loci (QTL) or gene(s) conferring resistance to FW, we constructed a genetic map of R. sativus using an F₂ mapping population derived by crossing the inbred lines ‘835’ (susceptible) and ‘B2’ (resistant). A total of 220 markers distributed in 9 linkage groups (LGs) were mapped in the Raphanus genome, covering a distance of 1,041.5 cM with an average distance between adjacent markers of 4.7 cM. Comparative analysis of the R. sativus genome with that of Arabidopsis thaliana and Brassica rapa revealed 21 and 22 conserved syntenic regions, respectively. QTL mapping detected a total of 8 loci conferring FW resistance that were distributed on 4 LGs, namely, 2, 3, 6, and 7 of the Raphanus genome. Of the detected QTL, 3 QTLs (2 on LG 3 and 1 on LG 7) were constitutively detected throughout the 2-year experiment. QTL analysis of LG 3, flanked by ACMP0609 and cnu_mBRPGM0085, showed a comparatively higher logarithm of the odds (LOD) value and percentage of phenotypic variation. Synteny analysis using the linked markers to this QTL showed homology to A. thaliana chromosome 3, which contains disease-resistance gene clusters, suggesting conservation of resistance genes between them.     

Identification of a single nucleotide deletion causing frameshift mutation in OsDFR2A in a genic male sterile mutant of rice and its possible application to F1 hybrid breeding

Stable genic male sterility (GMS), which is not influenced by environmental factors, has not been used for F₁ hybrid seed production because male-sterile inbred lines cannot be developed and male-sterile plants must be selected from segregating populations every time. However, the stability of male sterility may provide a reliable system for F₁ seed production without contamination of selfed seeds. A genic male-sterile mutant in rice (Oryza sativa L.), C204, which was selected from progeny of the cultivar ‘Koshihikari’ irradiated by gamma rays, has shorter and whiter anthers than those of ‘Koshihikari’ and has no pollen grains. Segregation analysis of C204 suggested the male sterility of this mutant to be controlled by a recessive allele of a single gene. Linkage analysis of a mutated gene responsible for the male sterility revealed the gene to be in a region of ca. 75 kb on the long arm of chromosome 9. The nine genes predicted in the 75-kb region were sequenced, and compared with the published Nipponbare genome sequences. A single-base deletion was found in the first exon of a C204 allele of Os09g0493500, which encodes an NAD-dependent epimerase/dehydratase family protein, resulting in a frameshift causing a premature stop codon. A dot-blot single nucleotide polymorphism marker for detection of the single-base deletion in Os09g0493500 was developed. We herein propose an F₁ hybrid seed production system using stable GMS with a simple selection method of GMS plants.     

Mapping of the genomic regions controlling seed storability in soybean (Glycine max L.)

Seed storability is especially important in the tropics due to high temperature and relative humidity of storage environment that cause rapid deterioration of seeds in storage. The objective of this study was to use SSR markers to identify genomic regions associated with quantitative trait loci (QTLs) controlling seed storability based on relative germination rate in the F_2:3 population derived from a cross between vegetable soybean line (MJ0004-6) with poor longevity and landrace cultivar from Myanmar (R18500) with good longevity. The F_2:4 seeds harvested in 2011 and 2012 were used to investigate seed storability. The F₂ population was genotyped with 148 markers and the genetic map consisted of 128 SSR loci which converged into 38 linkage groups covering 1664.3 cM of soybean genome. Single marker analysis revealed that 13 markers from six linkage groups (C1, D2, E, F, J and L) were associated with seed storability. Composite interval mapping identified a total of three QTLs on linkage groups C1, F and L with phenotypic variance explained ranging from 8.79 to 13.43%. The R18500 alleles increased seed storability at all of the detected QTLs. No common QTLs were found for storability of seeds harvested in 2011 and 2012. This study agreed with previous reports in other crops that genotype by environment interaction plays an important role in expression of seed storability.     

EVOLUTION OF BRASSICA RAPA L. (CRUCIFERAE) POPULATIONS IN INTRA- AND INTERSPECIFIC COMPETITION

Populations of Brassica rapa were grown for three generations in each of two environments: intraspecific competition, with four surrounding Brassica rapa neighbors per pot, and interspecific competition, with two Raphanus sativus neighbors per pot. In each environment, the largest (by flower number) 10% of the plants were outcrossed and provided seeds for the next generation. As a control, a randomly chosen 10% of the plants in each environment were outcrossed to produce seed for the next generation. Each of these four treatments, the selected lines in intra- and interspecific competition and the corresponding control lines, was maintained for three generations. After a single generation of growth in a common, no-competition environment, replicate plants from each treatment were grown with no competition and with intra- and interspecific competition for determination of growth responses. After two generations of selection, flower number in the intraspecific-selection line had increased by more than 50% over that in the control line and by more than 19% over that under interspecific selection. After a common-environment generation, plants from the intraspecific-selection line were shown to have significantly faster growth in height and flower number as seedlings. Plants in the interspecific-selection line showed similar but nonsignificant trends. No differences in seed mass, emergence time, or photosynthetic rate were found between control and selected lines in either intra- or interspecific competition. Some differences between control and selected lines were noted in biomass allocation related to differences in phenology. The results demonstrate that performance in competitive environments can evolve through changes in plant development but that rates of evolution will differ in intra- and interspecific competition.     

Mapping loci controlling vernalization requirement in Brassica rapa

Brassica cultivars are classified as biennial or annual based on their requirement for a period of cold treatment (vernalization) to induce flowering. Genes controlling the vernalization requirement were identified in a Brassica rapa F₂ population derived from a cross between an annual and a biennial oilseed cultivar by using an RFLP linkage map and quantitative trait locus (QTL) analysis of flowering time in F₃ lines. Two genomic regions were strongly associated with variation for flowering time of unvernalized plants and alleles from the biennial parent in these regions delayed flowering. These QTLs had no significant effect on flowering time after plants were vernalized for 6 weeks, suggesting that they control flowering time through the requirement for vernalization. The two B. rapa linkage groups containing these QTLs had RFLP loci in common with two B. napus linkage groups that were shown previously to contain QTLs for flowering time. An RFLP locus detected by the cold-induced gene COR6.6 cloned from Arabidopsis thaliana mapped very near to one of the B. rapa QTLs for flowering time.     

Identification of loci associated with embryo yield in microspore culture of <Emphasis Type="Italic">Brassica rapa</Emphasis> by segregation distortion analysis

Key message

We identified three physical positions associated with embryo yield in microspore culture of Brassica rapa by segregation distortion analysis. We also confirmed their genetic effects on the embryo yield.

Abstract

Isolated microspore culture is well utilized for the production of haploid or doubled-haploid plants in Brassica crops. Brassica rapa cv. ‘Ho Mei’ is one of the most excellent cultivars in embryo yield of microspore culture. To identify the loci associated with microspore embryogenesis, segregation analysis of 154 DNA markers anchored to B. rapa chromosomes (A01–A10) was performed using a population of microspore-derived embryos obtained from an F₁ hybrid between ‘CR-Seiga’, a low yield cultivar in microspore-derived embryos, and ‘Ho Mei’. Three regions showing significant segregation distortion with increasing ‘Ho Mei’ alleles were detected on A05, A08 and A09, although these regions showed the expected Mendelian segregation ratio in an F₂ population. The additive effect of alleles in these regions on embryo yield was confirmed in a BC₃F₁ population. One region on A08 containing Br071-5c had a higher effect than the other regions. Polymorphism of nucleotide sequences around the Br071-5c locus was investigated to find the gene possibly responsible for efficient embryogenesis from microspores.

     

A comprehensive and precise set of intervarietal substitution lines to identify candidate genes and quantitative trait loci in oilseed rape (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Key message

A set of intervarietal substitution lines were developed in rapeseed by recurrent backcrossing and marker-assisted selection and employed for mapping both qualitative and quantitative traits.

Abstract

Intervarietal substitution lines (ISLs) may be assembled into advanced secondary mapping populations that have remarkable potential for resolving trait loci and mapping candidate genes. To facilitate the identification of important genes in oilseed rape (canola, Brassica napus), we developed 89 ISLs using an elite cultivar ‘Zhongyou 821’ (ZY821) as the recipient and a re-synthesized line ‘No.2127’ as the donor. In the whole process of ISLs development, the target chromosome segments were selected based on the genotypes of 300 microsatellite markers evenly distributed across the genome. Eighty-nine ISLs fixed at BC₅F₄ were genotyped by sequencing using double digestion to survey the lengths of target substitution segments from the donor parent and the background segments from the recurrent parent. The total length of the substituted chromosome segments was 3030.27 Mb, representing 3.56?×?of the Darmor-bzh reference genome sequence (version 4.1). Gene mapping was conducted for two qualitative traits, flower colour and seed-coat colour, and nine quantitative traits including yield- and quality-related traits, with 19 QTLs identified for the latter. Overlapping substitution segments were identified for flower colour and seed-coat colour loci, as well as for QTLs consistently detected in 2 or 3 years. These results demonstrate the value of these ISLs for locus resolution and subsequent cloning, targeted mutation or editing of genes controlling important traits in oilseed rape.

     

超甜玉米种子萌发物质利用性状杂种优势及亲子回归关系分析

为阐明超甜玉米(Zea mays L.var.saccharata Bailey)亲本对F_1种子物质利用性状遗传效应,研究了19份自交系和其测配的10个杂交组合的杂种优势及亲子回归关系。结果表明,超甜玉米自交系及F_1种子的淀粉含量、蛋白质含量、脂肪含量、百粒重、种子物质动用量和种子物质利用率差异较大,10个杂交组合中亲本和F_1种子的淀粉含量、脂肪含量、百粒重均存在显著差异。F_1种子淀粉含量和百粒重均表现出正向超亲优势,即近高亲本遗传;而F_1种子的蛋白质含量、脂肪含量、种子物质动用量和种子物质利用率为近低亲本遗传。聚类分析和杂种优势分析表明,性状差异较大的FH14、Q26、GT22、GT2等亲本测配的杂交组合在种子百粒重或种子物质利用率等性状上具有较强的超亲优势。回归分析表明,母本对F_1种子的淀粉含量、百粒重有负效应,对种子物质动用量和种子物质利用率有正效应;父本对种子淀粉含量有负效应,对种子物质利用率有正效应。     

Analysis of QTLs for emcic acid and oil content in seeds on A8 chro- mosome and the linkage drag between the alleles for the two traits in Brassica napus

The history of canola breeding began with the discovery of germplasm with low erucic acid content in seeds of spring forage cultivar in the 1950's. FAE1 mutations led to a dramatic decrease of the seed erucic acid content in Arabidopsis thaliana. The products of the two FAE1 loci, BnA8.FAE1 and BnC3.FAE1, showed additive effects to the level of erucic acid content in oilseed rape. Previous research believed that the pleiotropy of FAE1 was responsible for the decrease in seed oil content along with the reduction of seed erucic acid content in the modern cultivars. TN DH population was developed from a canola cultivar Tapidor and a Chinese traditional cultivar Ningyou7. The population had been tested in 10 and 11 environments to map QTLs for the erucic acid content and oil content in seeds. As the map resolution increased, a novel QTL for seed erucic acid content was revealed, after Meta-analysis, 7 cM away from the most significant seed erucic acid content QTL where BnA8.FAE1 is located. Seven independent QTLs for seed oil content (qOC) were detected around the two seed erucic acid content QTLs (qEA) across 39.20 cM on linkage group A8. Two of the qOCs co-localized with the two qEAs, respectively, and were detected in a single environment. The other five qOCs were detected in 10 of 11 environments independent of qEAs. Alleles from Tapidor in all the QTLs at the 0–39.20 cM region contributed negative effects to either erucic acid content or oil content in seeds. Parallel, genotyping showed that on 5 of the 7 QTLs regions, Tapidor alleles had the same genotypes with that in ‘Liho’, the original low seed erucic acid content source. Through rounds of crossbreeding with oil-cropped cultivars and intensive selection for multi generations, Tapidor still had the inferior alleles for low seed oil content from ‘Liho’, the forage rape. This showed a strong linkage drag of low seed oil content, which was controlled by the five qEA-independent qOCs, with low seed erucic acid content. Ninety cultivars of B. napus from 8 countries were used to analyze the genetic drag with 9 molecular markers located in the QTL confidence intervals (24.04 cM) on linkage group A8. It was noticed that more than 46% of the cultivars with low seed erucic acid content trait remained the genotype of low seed oil content at least in one locus. Backcross and marker-assisted selection could break the genetic drag between the low oil content and erucic acid in seeds in the process for breeding modern high seed oil content canola cultivars.     

Origin of new <Emphasis Type="Italic">Brassica</Emphasis> types from a single intergeneric hybrid between <Emphasis Type="Italic">B. rapa</Emphasis> and <Emphasis Type="Italic">Orychophragmus violaceus</Emphasis> by rapid chromosome evolution and introgression

Many novel lines were established from an intergeneric mixoploid between Brassica rapa (2n = 20) and Orychophragmus violaceus (2n = 24) through successive selections for fertility and viability. Pedigrees of individual F₂ plants were advanced to the 10th generation by selfing. Their breeding habit was self-compatible and different from the self-incompatibility of their female parent B. rapa, and these lines were reproductively isolated to different degrees from B. rapa and B. napus. The lines with high productivity showed not only a wide spectrum of phenotypes but also obvious variations in fatty acid profiles of seed oil and glucosinolate contents in seed meal. These lines had 2n = 36, 37, 38, 39 and 40, with 2n = 38 being most frequent (64.56%), and no intact O. violaceus chromosomes were detected by genomic in situ hybridization (GISH) analysis. Amplified fragment length polymorphism (AFLP) analyses revealed a high extent of variation in genomic compositions across all the lines. O. violaceus-specific bands, deleted bands in B. rapa and novel bands for two parents were detected in these lines, with novel bands being the most frequent. The morphological and genetic divergence of these novel types derived from a single hybrid is probably due to rapid chromosomal evolution and introgression, and provides new genetic resources for rapeseed breeding.     

Inheritance of a dwarf seed stalk character in onion

Results are reported of crossing a dwarf seed stalk line (mean height 44.8 cm) from Israel with five inbred lines of the Rijnsburger type each having normal tall seed stalks (mean heights 83.1–105.9 cm). The seed stalk height of F₁ generations from these crosses was slightly greater than that of the Rijnsburger parents but segregation occurred in the F₂ giving plants which could be considered ‘dwarf’ and ‘normal’ with respect to seed stalk height. Selfing individual F₂‘dwarf’ plants produced F₃ progenies whose mean heights were in the dwarf range, and were significantly correlated with those of their F₂ parent. The results obtained in the F₂ and F₃ families suggest that although a major recessive gene for dwarfness may be present, substantial minor gene and environmental variation is also involved.     

Identification of Novel QTLs for Isolate-Specific Partial Resistance to Plasmodiophora brassicae in Brassica rapa

Plasmodiophora brassicae, the causal agent of clubroot disease of the Brassica crops, is widespread in the world. Quantitative trait loci (QTLs) for partial resistance to 4 different isolates of P. brassicae (Pb2, Pb4, Pb7, and Pb10) were investigated using a BC₁F₁ population from a cross between two subspecies of Brassica rapa, i.e. Chinese cabbage inbred line C59-1 as a susceptible recurrent parent and turnip inbred line ECD04 as a resistant donor parent. The BC₁F₂ families were assessed for resistance under controlled conditions. A linkage map constructed with simple sequence repeats (SSR), unigene-derived microsatellite (UGMS) markers, and specific markers linked to published clubroot resistance (CR) genes of B. rapa was used to perform QTL mapping. A total of 6 QTLs residing in 5 CR QTL regions of the B. rapa chromosomes A01, A03, and A08 were identified to account for 12.2 to 35.2% of the phenotypic variance. Two QTL regions were found to be novel except for 3 QTLs in the respective regions of previously identified Crr1, Crr2, and Crr3. QTL mapping results indicated that 1 QTL region was common for partial resistance to the 2 isolates of Pb2 and Pb7, whereas the others were specific for each isolate. Additionally, synteny analysis between B. rapa and Arabidopsis thaliana revealed that all CR QTL regions were aligned to a single conserved crucifer blocks (U, F, and R) on 3 Arabidopsis chromosomes where 2 CR QTLs were detected in A. thaliana. These results suggest that some common ancestral genomic regions were involved in the evolution of CR genes in B. rapa.     

Tetralocular ovary and high silique width in yellow sarson lines of Brassica rapa (subspecies trilocularis) are due to a mutation in Bra034340 gene,a homologue of CLAVATA3 in Arabidopsis

Key message

Genetic locus for tetralocular ovary ( tet - o ) in Brassica rapa was identified and it was shown that the number of locules and width of silique are associated.

Abstract

Brassica rapa is a highly polymorphic species containing many vegetables and oleiferous types. An interesting group of oleiferous types is the yellow sarson group (subspecies trilocularis) grown mostly in eastern India. This group contains lines that have bilocular ovaries, a defining trait of Brassicaceae, but also lines that have tetralocular ovaries. Yellow sarson lines commonly have high silique width which is further enhanced in the tetralocular types. We mapped the locus influencing tetralocular ovary in B. rapa using three mapping populations (F₂, F₆ and F₇) derived from a cross between Chiifu (subspecies pekinensis, having bilocular ovary) and Tetralocular (having tetralocular ovary). QTL mapping of silique width was undertaken using the three mapping populations and a F₂ population derived from a cross between Chiifu and YSPB-24 (a bilocular line belonging to yellow sarson group). Qualitative mapping of the trait governing locule number (tet-o) in B. rapa mapped the locus to linkage group A4. QTL mapping for silique width detected a major QTL on LG A4, co-mapping with the tet-o locus in bilocular/tetralocular cross. This QTL was not detected in the bilocular/bilocular cross. Saturation mapping of the tet-o region with SNP markers identified Bra034340, a homologue of CLAVATA3 of Arabidopsis thaliana, as the candidate gene for locule number. A C → T transition at position 176 of the coding sequence of Bra034340 revealed co-segregation with the tetralocular phenotype. The study of silique related traits is of interest both for understanding evolution under artificial selection and for breeding of cultivated Brassica species.     

Developing stable progenies of ×Brassicoraphanus, an intergeneric allopolyploid between Brassica rapa and Raphanus sativus, through induced mutation using microspore culture

Induced mutations were used to improve the low seed fertility of an intergeneric allopolyploid, ‘Baemoochae,’ ×Brassicoraphanus, synthesized following hybridization between Brassica rapa and Raphanus sativus. The mutagen N-methyl-N-nitroso-urethane (NMU) was added to microspore cultures. Four lines of nine in the Mi₂ generation showed very high fertility under controlled pollination. The progeny lines (Mi₃) confirmed this result under open pollination, and excellent uniformity was observed in plants grown in the field, as well as in their AFLP profile. On attaining high fertility and uniformity, one of the lines was released to farmers as a new leafy vegetable crop. The original nine lines shared very similar AFLP banding patterns, without any large differences between the high and low seed fertility lines. Thus, mutation induction accelerated genetic stabilization of a newly synthesized allopolyploid, ×Brassicoraphanus.     

Development of carrot inbreds with resistance to carrot fly using a single seed descent programme

Two carrot cultivars, ‘Sytan’ and ‘Long Chantenay’, representing commercially important carrot types and selected for their partial resistance to the carrot fly (Psila rosae) were crossed as the basis for a single seed descent programme. The resulting F₁ progeny were mass pollinated to produce an F₂ generation and approximately 2000 plants were raised from this segregating family in the glasshouse in 1981. By careful choice of sowing date and glasshouse temperatures it was possible to stimulate the plants to flower within 10 months. Individual king umbels were enclosed within bags and pollinated with blowflies. Resulting seed was sown in pots in the following August and the process of seed production repeated in a 12 month cycle. Each inbred line was selfed in this way over three generations until the F₅ stage. Stocks of seed were then multiplied. A total of 753 inbreds were produced by 1987. The vigour of each inbred was evaluated in glasshouse tests and the level of chlorogenic acid was determined by a fluorescence technique. The most vigorous lines with the lowest levels of chlorogenic acid were tested in field experiments against carrot fly at Wellesbourne. Nine inbreds with promising agronomic quality and moderate resistance to carrot fly were selected and seeded. These nine lines were submitted to seed companies with the aim of developing new cultivars of carrot.     

Phenotyping at hot spots and tagging of QTLs conferring spot blotch resistance in bread wheat

Spot blotch is a major foliar disease of wheat caused by Bipolaris sorokiniana in warm and humid environments of the world including South Asian countries. In India, it has a larger impact in Indo-Gangetic plains of the country. Therefore, the present study was undertaken to phenotype a mapping population at different hot spots of India and to detect quantitative trait loci (QTL) for resistance to spot blotch in wheat. For this study, 209 single seed descent (SSD) derived F₈, F₉, F₁₀ recombinant inbred lines (RILs) of the cross ‘Sonalika’ (an Indian susceptible cultivar)/‘BH 1146’ (a Brazilian resistant cultivar) were assessed for spot blotch resistance at two hot spot locations (Coochbehar and Kalyani) for three years and for two years under controlled conditions in the polyhouse (Karnal). The population showed large variation in spot blotch reaction for disease severity in all the environments indicating polygenic nature of the disease. Microsatellite markers were used to create the linkage maps. Joint and/or individual year analysis by composite interval mapping (CIM) and likelihood of odds ratio (LOD) >2.1, detected two consistent QTLs mapped on chromosome 7BL and 7DL and these explained phenotypic variation of 11.4 percent and 9.5 percent over the years and locations, respectively. The resistance at these loci was contributed by the parent ‘BH 1146’ and shown to be independent of plant height and earliness. Besides, association of some agro-morphological traits has also been observed with percent disease severity. These identified genomic regions may be used in future wheat breeding programs through marker assisted selection for developing spot blotch resistant cultivars.     

Candidate genes underlying the quantitative trait loci for root-knot nematode resistance in a Cucumis hystrix introgression line of cucumber based on population sequencing

The southern root-knot nematode (RKN), Meloidogyne incognita (Kofoid & White) Chitwood, is one of most destructive species of plant parasitic nematodes, causing significant economic losses to numerous crops including cucumber (Cucumis sativus L. 2n = 14). No commercial cultivar is currently available with resistance to RKN, severely hindering the genetic improvement of RKN resistance in cucumber. An introgression line, IL10-1, derived from the interspecific hybridization between the wild species Cucumis hystrix Chakr. (2n = 24, HH) and cucumber, was identified with resistance to RKN. In this study, an ultrahigh-density genetic linkage bin-map, composed of high-quality single-nucleotide polymorphisms (SNPs), was constructed based on low-coverage sequences of the F_2:6 recombinant inbred lines derived from the cross between inbred line IL10-1 and cultivar ‘Beijingjietou’ CC3 (hereinafter referred to as CC3). Three QTLs were identified accounting for 13.36% (qRKN1-1), 9.07% and 9.58% (qRKN5-1 and qRKN5-2) of the resistance variation, respectively. Finally, four genes with nonsynonymous SNPs from chromosome 5 were speculated to be the candidate RKN-resistant related genes, with annotation involved in disease resistance. Though several gaps still exist on the bin-map, our results could potentially be used in breeding programs and establish an understanding of the associated mechanisms underlying RKN resistance in cucumber.

     

Increased pre-dispersal seed predation in sunflower crop-wild hybrids

The fitness of crop-wild hybrids can influence gene flow between crop and wild populations. Seed predation levels in crop-wild hybrid plants can be an important factor in determining plant fitness, especially in large-seeded crops such as sunflower. To determine patterns of pre-dispersal seed predation, seeds were collected from wild sunflowers (Helianthus annuus L.) and wild×crop F₁ hybrids at three experimental field sites in eastern Kansas. Seed heads were dissected and each seed was counted and scored for categories of seed damage by lepidopteran and coleopteran larvae. Hybrid seed heads showed significantly higher levels of insect-damaged seeds. The average hybrid plant had 36.5% of its seeds (or 45.1 seeds per plant) eaten by insect larvae while the average wild plant lost only 1.8% (or 95 seeds) to seed predators. Hybrid populations had higher levels of total insect damage even when date of flowering, flower head diameter, and the number of open heads within the study site were accounted for. These results suggest that the reduced fecundity of F₁ crop-wild sunflower hybrids demonstrated in other studies may be augmented by the increased seed predation in hybrid flower heads. Fecundity estimates of crop-wild hybrid and wild plants that disregard differential seed predation levels may not accurately reflect the actual relative contributions of hybrid and wild plants to future generations. Received: 21 December 1998 / Accepted: 8 July 1999     

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC₂F₂ population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2?cM, spanning 1,553.4?cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC₂F₂ families, 26 advanced backcross breeding lines (BC₂F₅) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC₂F₃ and BC₂F₄ generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC₂F₅ generation whereas 29 QTLs were detected in BC₂F₂ generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R ² values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC₂F₅ population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.     

Genetic mapping and validation of the loci controlling 7S α′ and 11S A-type storage protein subunits in soybean [<Emphasis Type="Italic">Glycine max</Emphasis> (L.) Merr.]

Key message

Four soybean storage protein subunit QTLs were mapped using bulked segregant analysis and an F₂ population, which were validated with an F₅ RIL population.

Abstract

The storage protein globulins β-conglycinin (7S subunit) and glycinin (11S subunits) can affect the quantity and quality of proteins found in soybean seeds and account for more than 70% of the total soybean protein. Manipulating the storage protein subunits to enhance soymeal nutrition and for desirable tofu manufacturing characteristics are two end-use quality goals in soybean breeding programs. To aid in developing soybean cultivars with desired seed composition, an F₂ mapping population (n = 448) and an F₅ RIL population (n = 180) were developed by crossing high protein cultivar ‘Harovinton’ with the breeding line SQ97-0263_3-1a, which lacks the 7S α′, 11S A₁, 11S A₂, 11S A₃ and 11S A₄ subunits. The storage protein composition of each individual in the F₂ and F₅ populations were profiled using SDS-PAGE. Based on the presence/absence of the subunits, genomic DNA bulks were formed among the F₂ plants to identify genomic regions controlling the 7S α′ and 11S protein subunits. By utilizing polymorphic SNPs between the bulks characterized with Illumina SoySNP50K iSelect BeadChips at targeted genomic regions, KASP assays were designed and used to map QTLs causing the loss of the subunits. Soybean storage protein QTLs were identified on Chromosome 3 (11S A₁), Chromosome 10 (7S α′ and 11S A₄), and Chromosome 13 (11S A₃), which were also validated in the F₅ RIL population. The results of this research could allow for the deployment of marker-assisted selection for desired storage protein subunits by screening breeding populations using the SNPs linked with the subunits of interest.