Proline concentration has been often suggested as an indicator of osmotic stress. A better understanding of the genetics of this trait is however needed. In the present study, proline concentration has been assessed, together with root and stem growth, potassium, calcium and total soluble sugars concentration and stress injury symptoms, in seedlings of sunflower hybrids and their parents grown under control and osmotic conditions. Proline strongly accumulated with osmotic stress. Its concentration exhibited a large variation among genotypes and was higher in hybrids than in parental lines. A positive association was noted between proline concentration and osmotic adjustment that was reflected in a reduction of osmotic stress induced injury, as showed by the reduced number of calli in the hybrids with higher proline concentration. Broad and narrow sense heritability was higher under osmotic stress suggesting applying the selection in osmotic stress condition. In the control treatment, dominance effects explained most of the genetic variation for proline concentration while under osmotic stress both dominance and additive variance were high. The importance of dominance and additive effects suggested that several genomic regions are controlling this trait. Good general combiners, presumably carrying positive additive alleles affecting proline concentration, were identified.
A quantitative trait locus (QTL) controlling wheat grain protein content (GPC) and flour protein content (FPC) was identified using doubled haploid (DH) lines developed from a cross between the hard red winter wheat variety ‘Yumechikara’ with a high protein content used for bread making, and the soft red winter wheat ‘Kitahonami’ with a low protein content used for Japanese white salted noodles. A single major QTL, QGpc.2B-yume, was identified on the short arm of wheat chromosome 2B for both the GPC and FPC over 3 years of testing. QGpc.2B-yume was mapped on the flanking region of microsatellite marker Xgpw4382. The DH lines grouped by the haplotype of the closest flanking microsatellite marker Xgpw4382 showed differences of 1.0% and 1.1% in mean GPC and FPC, respectively. Yield-component-related traits were not affected by the haplotype of QGpc.2B-yume, and major North American hard red winter wheat varieties showed the high-protein haplotype. Unlike Gpc-B1 derived from tetraploid wheat, QGpc.2B-yume has no negative effects on yield-component-related traits and should be useful for wheat breeding to increase GPC and FPC.
Foods rich in resistant starch can help prevent various diseases, including diabetes, colon cancers, diarrhea, and chronic renal and hepatic diseases. Variations in starch biosynthesis enzymes could contribute to the high content of resistant starch in some cultivars of rice (Oryza sativa L.). Our previously published work indicated that the sbe3-rs gene in the rice mutant line, ‘Jiangtangdao1’ was a putative allele of the rice starch branching enzyme gene SBEIIb (previously known as SBE3); sbe3-rs might control the biosynthesis of the high resistant starch content in the rice line. Biomolecular analysis showed that the activity of SBEs was significantly lower in soluble extracts of immature seeds harvested from ‘Jiangtangdao1’ 15 days after flowering than in the extracts of the wild-type rice line ‘Huaqingdao’. We performed gene complementation assays by introducing the wild-type OsSBEIIb into the sbe3-rs mutant ‘Jiangtangdao1’. The genetically complemented lines demonstrated restored seed-related traits. The structures of endosperm amylopectin and the morphological and physicochemical properties of the starch granules in the transformants recovered to wild-type levels. This study provides evidence that sbe3-rs is a novel allele of OsSBEIIb, responsible for biosynthesis of high resistant starch in ‘Jiangtangdao1’.
Shiikuwasha (Citrus depressa Hayata) is distributed from the South-west of the Japanese archipelago to Taiwan. In this study, re-sequencing against the orange (C. sinensis (L.) Osbeck) chloroplast genome was applied to one superior landrace of Shiikuwasha cultivated in Oku ward, Okinawa, Japan. The chloroplast genome of the landrace was estimated to comprise 160,118 bp, including 48 indels and 71 nucleotide substitutions against the reference genome. The presumptive chloroplast indels were confirmed by subsequent experiments, and these identified multiple maternal lineages among other landraces. Some of the orange SSR markers were available for genotyping of other superior landraces and were able to distinguish among them. These molecular markers were then applied for evaluation of genetic diversity among wild and cultivated Shiikuwasha accessions. Except for Oku ward, the cultivated populations were found to have lost their genetic diversity in comparison with wild populations. Groves in Oku ward maintained, or showed even higher genetic diversity than wild accessions in the surrounding areas by the force of villagers.
‘Fuji’ is one of the most popular and highly-produced apple cultivars worldwide, and has been frequently used in breeding programs. The development of genotypic markers for the preferable phenotypes of ‘Fuji’ is required. Here, we aimed to define the haplotypes of ‘Fuji’ and find associations between haplotypes and phenotypes of five traits (harvest day, fruit weight, acidity, degree of watercore, and flesh mealiness) by using 115 accessions related to ‘Fuji’. Through the re-sequencing of ‘Fuji’ genome, total of 2,820,759 variants, including single nucleotide polymorphisms (SNPs) and insertions or deletions (indels) were detected between ‘Fuji’ and ‘Golden Delicious’ reference genome. We selected mapping-validated 1,014 SNPs, most of which were heterozygous in ‘Fuji’ and capable of distinguishing alleles inherited from the parents of ‘Fuji’ (i.e., ‘Ralls Janet’ and ‘Delicious’). We used these SNPs to define the haplotypes of ‘Fuji’ and trace their inheritance in relatives, which were shown to have an average of 27% of ‘Fuji’ genome. Analysis of variance (ANOVA) based on ‘Fuji’ haplotypes identified one quantitative trait loci (QTL) each for harvest time, acidity, degree of watercore, and mealiness. A haplotype from ‘Delicious’ chr14 was considered to dominantly cause watercore, and one from ‘Ralls Janet’ chr1 was related to low-mealiness.
Resynthesized (RS) oilseed rape (Brassica napus L.) is potentially of great interest for hybrid breeding. However, a major problem with the direct use of RS B. napus is the quality of seed oil (high level of erucic acid) and seed meal (high glucosinolate content), which does not comply with double-low quality oilseed rape. Thus, additional developments are needed before RS B. napus can be introduced into breeding practice. In this study, RS oilseed rape was obtained through crosses between B. rapa ssp. chinensis var. chinensis and B. oleracea ssp. acephala var. sabellica. RS plant was then crossed with double-low (00) winter oilseed rape lines containing the Rfo gene for Ogura cytoplasmic male sterility (CMS ogu) system. Populations of doubled haploids (DH) were developed from these F1 hybrids using the microspore in vitro culture method. The seeds of semi-RS DH lines were analyzed for erucic acid and glucosinolate content. Among the populations of semi-RS DHs four 00-quality lines with the Rfo gene were selected. Using 344 AFLP markers to estimate genetic relatedness, we showed that the RS lines and semi-RS lines formed clusters that were clearly distinct from 96 winter oilseed rape parental lines of F1 hybrids.
Aegilops variabilis (UUSvSv), an important sources for wheat improvement, originated from chromosome doubling of a natural hybrid between Ae. umbellulata (UU) with Ae. longissima (SlSl). The Ae. variabilis karyotype was poorly characterized by fluorescent in situ hybridization (FISH). The FISH probe combination of pSc119.2, pTa71 and pTa-713 identified each of the 14 pairs of Ae. variabilis chromosomes. Our FISH ideogram was further used to detect an Ae. variabilis chromosome carrying stripe rust resistance in the background of wheat lines developed from crosses of the stripe rust susceptible bread wheat cultivar Yiyuan 2 with a resistant Ae. variabilis accession. Among the 15 resistant BC1F7 lines, three were 2Sv + 4Sv addition lines (2n = 46) and 12 were 2Sv(2B) or 2Sv(2D) substitution lines that were confirmed with SSR markers. SSR marker gwm148 can be used to trace 2Sv in common wheat background. Chromosome 2Sv probably carries gametocidal(Gc) gene(s) since cytological instability and chromosome structural variations, including non-homologous translocations, were observed in some lines with this chromosome. Due to the effects of photoperiod genes, substitution lines 2Sv(2D) and 2Sv(2B) exhibited late heading with 2Sv(2D) lines being later than 2Sv(2B) lines. 2Sv(2D) substitution lines were also taller and exhibited higher spikelet numbers and longer spikes.
Salt tolerance in soybean [Glycine max (L.) Merr.] at the seed germination stage is a critical determinant of stable stand establishment in saline soil. This study examined one population of 184 recombinant inbred lines (RILs, F7:11) derived from a cross between Kefeng1 and Nannong1138-2 and one natural population consisting of 196 soybean landraces. A total of 11 quantitative trait loci (QTLs) and 22 simple sequence repeat (SSR) loci associated with three salt tolerance indices were detected by linkage and association mapping. The SSR marker Sat_162 was found to be closely linked to the co-localized QTLs at a site 792,811 bp from the gene Glyma08g12400.1, which was verified in response to salt stress at the germination stage. Five SSR markers, Satt201, BE475343, CSSR306, Satt664 and Satt567, were co-associated with two of the salt tolerance indices, and two SSR markers, Satt156 and Satt636, were co-associated with all three salt tolerance indices. Furthermore, elite alleles and their carrier materials were identified by analyzing alleles at the loci associated with these salt tolerance indices. These results may be beneficial for the future breeding of soybean salt tolerance at the germination stage using marker-assisted selection and molecular pyramiding breeding.
A new plant breeding method—the biotron breeding system (BBS)—can rapidly produce advanced generations in rice (Oryza sativa L.) breeding. This method uses a growth chamber (biotron) with CO2 control, accompanied by tiller removal and embryo rescue to decrease the period before seed maturity. However, tiller removal and embryo rescue are laborious and impractical for large populations. We investigated the influences of increased CO2, tiller removal, and root restriction on the days to heading (DTH) from seeding in growth chambers. The higher CO2 concentration significantly decreased DTH, but tiller removal and root restriction had little effect on DTH and drastically reduced seed yield. Based on these findings, we propose a simplified BBS (the sBBS) that eliminates the need for tiller removal and embryo rescue, but controls CO2 levels and day-length and maintains an appropriate root volume. Using the sBBS, we could reduce the interval between generations in ‘Nipponbare’ to less than 3 months, without onerous manipulations. To demonstrate the feasibility of the sBBS, we used it to develop isogenic lines using ‘Oborozuki’ as the donor parent for the low-amylose allele Wx1-1 and ‘Akidawara’ as the recipient. We were able to perform four crossing cycles in a year.
Doubled haploid (DH) populations, particularly those from subspecies crosses possessing the wide compatible gene S5n, are important germplasm resources for rice genetic studies and breeding, but their feature and potential have not been fully assessed and explored. In the present study, we produced a DH population from the hybrid of japonica 668B and wide compatible indica T23. Genotyping of the S5 locus with allele-specific markers for ORF3, ORF4 and ORF5 revealed a potential recombination hot spot in the ORF3-ORF4 region. Haplotyping analysis revealed that 21/34 subspecies specific Indel markers segregated in distortion in the DH population, with a few lines having indica alleles either extremely low (1.7%) or high (98.3%), with little effect of the S5 allele. While DH lines with the S5n allele had higher frequency of indica alleles, no effect of the S5n allele was observed on all agronomic traits but flowering time. Taken together, the present study advanced understanding of the genetics of wide crosses in general, and DH production in particular between the two rice subspecies, and the new DH population generated will become a useful resource for rice genetic study and breeding in the future.
Robert Sezi Kawuki, Tadeo Kaweesi, Williams Esuma, Anthony Pariyo, Ismail Siraj Kayondo, Alfred Ozimati, Vincent Kyaligonza, Alex Abaca, Joseph Orone, Robooni Tumuhimbise, Ephraim Nuwamanya, Philip Abidrabo, Teddy Amuge, Emmanuel Ogwok, Geoffrey Okao, Henry Wagaba, Gerald Adiga, Titus Alicai, Christopher Omongo, Anton Bua, Morag Ferguson, Edward Kanju, Yona Baguma
Cassava (Manihot esculenta Crantz) production is currently under threat from cassava brown streak disease (CBSD), a disease that is among the seven most serious obstacles to world’s food security. Three issues are of significance for CBSD. Firstly, the virus associated with CBSD, has co-evolved with cassava outside its center of origin for at least 90 years. Secondly, that for the last 74 years, CBSD was only limited to the low lands. Thirdly, that most research has largely focused on CBSD epidemiology and virus diversity. Accordingly, this paper focuses on CBSD genetics and/or breeding and hence, presents empirical data generated in the past 11 years of cassava breeding in Uganda. Specifically, this paper provides: 1) empirical data on CBSD resistance screening efforts to identify sources of resistance and/or tolerance; 2) an update on CBSD resistance population development comprising of full-sibs, half-sibs and S1 families and their respective field performances; and 3) insights into chromosomal regions and genes involved in CBSD resistance based on genome wide association analysis. It is expected that this information will provide a foundation for harmonizing on-going CBSD breeding efforts and consequently, inform the future breeding interventions aimed at combating CBSD.
Starch represents a major nutrient in the human diet providing essentially a source of energy. More recently the modification of its composition has been associated with new functionalities both at the nutritional and technological level. Targeting the major starch biosynthetic enzymes has been shown to be a valuable strategy to manipulate the amylose-amylopectin ratio in reserve starch. In the present work a breeding strategy aiming to produce a set of SSIIa (starch synthases IIa) null durum wheat is described. We have characterized major traits such as seed weight, total starch, amylose, protein and β-glucan content in a set of mutant families derived from the introgression of the SSIIa null trait into Svevo, an elite Italian durum wheat cultivar. A large degree of variability was detected and used to select wheat lines with either improved quality traits or agronomic performances. Semolina of a set of two SSIIa null lines showed new rheological behavior and an increased content of all major dietary fiber components, namely arabinoxylans, β-glucans and resistant starch. Furthermore the investigation of gene expression highlighted important differences in some genes involved in starch and β-glucans biosynthesis.
A glutinous texture of endosperm is one of the important traits of rice (Oyza sativa L.). Northern Laos is known as a center of glutinous rice diversity. We genotyped INDEL, SSR and SNP markers in a sample of 297 rice landraces collected in northern Laos. These glutinous varieties were confirmed to share a loss-of-function mutation in Granule bound starch synthase I (Wx). INDEL markers revealed a high frequency of recombinant genotypes between indica and japonica. Principal component analysis using SSR genotypes of Wx flanking region revealed that glutinous indica landraces were scattered between non-glutinous indica and glutinous-japonica types. High ratios of heterozygosity were found especially in glutinous indica. Haplotype analysis using SNP markers around Wx locus revealed that glutinous indica landraces would have a few chromosome segments of glutinous japonica. Frequent recombinations were confirmed outside of this region in glutinous indica. This intricate genetic structure of landraces suggested that glutinous indica landraces in Laos were generated through repeated natural crossing with glutinous-japonica landraces and severe selection by local farmers.
Gene pyramiding is an efficient approach for the genetic improvement of multiple agronomic traits simultaneously. In this study, we pyramided two foreign genes, cry1Ac driven by the rice Actin I promoter, and lysine-rich protein (LRP), driven by the endosperm-specific GLUTELIN1 (GT1) promoter, into the elite indica cultivar 9311. These two genes were chosen in an attempt to enhance insect-resistance and Lysine (Lys) content. In the pyramided line, the foreign gene cry1Ac was efficiently expressed in the leaves and stems, and exhibited highly efficient resistance to striped stem borer (SSB, Chilo suppressalis Walker) in the laboratory and rice leaf folder (RLF, Cnaphalocrocis medinalis Guenee) in the field. Furthermore, the LRP gene was highly expressed in the endosperm and produced a remarkable increase of Lys content in the seeds of the pyramided line. The data from field trials demonstrated that most of the agronomic traits including yield were well maintained in the pyramided line compared to the parental control. These results strongly suggest that the foreign cry1Ac and LRP genes have remarkable application potential in rice, and the resultant pyramided line serves as an ideal bridge material for the improvement of insect-resistance and high Lys rice in the future.
Rice is one of mankind’s major food staples, and the erect panicle architecture in rice is an important morphological improvement. The dense and erect panicle 1 (DEP1) locus corresponds with the formation of erect panicles and has been widely used in rice breeding. However, the genetic diversity of DEP1 remains narrow. In order to improve the genetic diversity of DEP1, we used a rice germplasm collection of 72 high yielding japonica rice varieties to analyze the contribution of DEP1 to the panicle traits. We found 45 SNPs and 26 insertions and deletions (indels) within the DNA fragment of DEP1. We further detected 7 haplotypes and found that the replacement of 637 bp by a 12 bp fragment could explain the erect panicle architecture in all 72 germplasms. An SNP (G/C) at the -1253 bp of the promoter region caused a core sequence shift (TGGGCC) of a site II transcriptional regulatory element. The association analysis showed that the SNP(G/C) largely affects the number of primary and secondary branches, and grain number per panicle. Our results provide novel insights into the function and genetic diversity of DEP1. The SNP (G/C) at the promoter region will contribute to the flexible application of DEP1 in rice breeding.
Successful haploid induction in loquat (Eriobotrya japonica (Thunb.) Lindl.) through in situ-induced parthenogenesis with gamma-ray irradiated pollen has been achieved. Female flowers of cultivar ‘Algerie’ were pollinated using pollen of cultivars ‘Changhong-3’, ‘Cox’ and ‘Saval Brasil’ irradiated with two doses of gamma rays, 150 and 300 Gy. The fruits were harvested 90, 105 and 120 days after pollination (dap). Four haploid plants were obtained from ‘Algerie’ pollinated with 300-Gy-treated pollen of ‘Saval Brasil’ from fruits harvested 105 dap. Haploidy was confirmed by flow cytometry and chromosome count. The haploids showed a very weak development compared to the diploid plants. This result suggests that irradiated pollen can be used to obtain parthenogenetic haploids.
Sheath blight is considered the most significant disease of rice and causes enormous yield losses over the world. Breeding for resistant varieties is the only viable option to combat the disease efficiently. Seventeen diverged rice genotypes along with 17 QTL-linked SSR markers were evaluated under greenhouse conditions. Pearson’s correlation showed only the flag leaf angle had a significant correlation with sheath blight resistance under greenhouse screening. Multivariate analysis based on UPGMA clustering and principal component analysis (PCA) indicated that the flag leaf angle, flag leaf length, and plant compactness were significantly associated with the following SSR marker alleles: RM209 (116,130), RM202 (176), RM224 (126), RM257 (156), RM426 (175), and RM6971 (196), which are linked to the SB QTLs: QRlh11, qSBR11-3, qSBR11-1, qSBR9-1, qShB3-2, and qSB-9. A Mantel test suggested a weak relationship between the observed phenotypes and allelic variation patterns, implying the independent nature of morphological and molecular variations. Teqing and Tetep were found to be the most resistant cultivars. IR65482-4-136-2-2, MR219-4, and MR264 showed improved resistance potentials. These results suggest that the morphological traits and QTLs which have been found to associate with sheath blight resistance are a good choice to enhance resistance through pyramiding either 2 QTLs or QTLs and traits in susceptible rice cultivars.
Global efforts are underway to biofortify cassava (Manihot esculenta Crantz) with provitamin A carotenoids to help combat dietary vitamin A deficiency afflicting the health of more than 500 million resource-poor people in Sub-Saharan Africa. To further the biofortification initiative in Uganda, a 6×6 diallel analysis was conducted to estimate combining ability of six provitamin A clones and gene actions controlling total carotenoid content (TCC), dry matter content (DMC) in cassava roots and other relevant traits. Fifteen F1 families generated from the diallel crosses were evaluated in two environments using a randomized complete block design. General combining ability (GCA) effects were significant for TCC and DMC, suggesting the relative importance of additive gene effects in controlling these traits in cassava. On the other hand, non-additive effects were predominant for root and shoot weight. MH02-073HS, with the highest level of TCC, was the best general combiner for TCC while NASE 3, a popular white-fleshed variety grown by farmers in Uganda, was the best general combiner for DMC. Such progenitors with superior GCA effects could form the genetic source for future programs targeting cassava breeding for TCC and DMC. A negative correlation was observed between TCC and DMC, which will require breeding strategies to combine both traits for increased adoption of provitamin A cassava varieties.
Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is a chief factor limiting rice productivity worldwide. XM14, a rice mutant line resistant to Xoo, has been obtained by treating IR24, which is susceptible to six Philippine Xoo races and six Japanese Xoo races, with N-methyl-N-nitrosourea. XM14 showed resistance to six Japanese Xoo races. The F2 population from XM14 × IR24 clearly showed 1 resistant : 3 susceptible segregation, suggesting control of resistance by a recessive gene. The approximate chromosomal location of the resistance gene was determined using 10 plants with shortest lesion length in the F2 population from XM14 × Koshihikari, which is susceptible to Japanese Xoo races. DNA marker-assisted analysis revealed that the gene was located on chromosome 3. IAS16 line carries IR24 genetic background with a Japonica cultivar Asominori segment of chromosome 3, on which the resistance gene locus was thought to be located. The F2 population from IAS16 × XM14 showed a discrete distribution. Linkage analysis indicated that the gene is located around the centromeric region. The resistance gene in XM14 was a new gene, named XA42. This gene is expected to be useful for resistance breeding programs and for genetic analysis of Xoo resistance.
Low molecular weight glutenin subunits are important components of wheat storage proteins, which play an important role in determining end-use quality of common wheat. A newly established matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) procedure was used to analyze 478 landraces of bread wheat collected from the Yangtze-River region in China. Results indicated that 17 alleles at three loci: Glu-A3, Glu-B3 and Glu-D3 were identified, resulting in 87 different allele combinations. Of the 17 alleles detected at all the Glu-3 loci, five belonged to Glu-A3, seven to Glu-B3 and five to Glu-D3 locus. MALDI-TOF-MS indicated Glu-A3a/c was present in 72.8%, Glu-A3b in 8.4%, Glu-A3d in 8.4%, Glu-A3f in 5.2% and Glu-A3e in 3.6% lines. Seven types of alleles were identified at the Glu-B3 locus: Glu-B3d/i (25.5%), Glu-B3b (21.3%), Glu-B3c (16.9%), Glu-B3h (13.8%), Glu-B3f (8.4%), Glu-B3a (8.2%), and Glu-B3g (5.2%). Five types of Glu-D3 alleles were detected: Glu-D3a (58.4%), Glu-D3c (22.6%), Glu-D3d (15.5%), Glu-D3b (3.3%) and Glu-D3f (0.2%). Four new alleles that showed abnormal MALDI-TOF spectrum patterns were identified at the Glu-A3 and Glu-B3 loci. A detailed study is needed to further characterize these alleles and their potential usage for wheat improvement.
Alpha-tocopherol is one of four tocopherol isoforms and has the highest vitamin E activity in humans. Most cultivated soybean seeds contain γ-tocopherol as the predominant form, and the ratio of α-tocopherol content to total tocopherol content (α-tocopherol ratio) is <10%. Three soybean accessions from Eastern Europe have α-tocopherol ratios of >20%. This higher content is likely due to mutations in the promoter region of the γ-tocopherol methytransferase-3 (γ-TMT3) gene. We surveyed a wild soybean germplasm collection and detected 16 accessions with stable seed α-tocopherol ratios of >20% under different growth conditions. The α-tocopherol ratios were greatly reduced when the plants were grown under cool temperatures during seed maturation, but increased to varying degrees at higher temperatures. Sequence analysis of the γ-TMT3 promoter of 11 of the accessions identified four haplotypes, one of which corresponded to that of cultivars with higher contents. These wild accessions can thus serve as novel donors for breeding cultivars with high α-tocopherol ratios and for better understanding the genetic basis of α-tocopherol synthesis in soybean.