Capsanthin, the main carotenoid of red pepper fruits, is beneficial for human health. To breed pepper (Capsicum annuum L.) with high capsanthin content by marker-assisted selection, we constructed a linkage map of doubled-haploid (DH) lines derived from a cross of two pure lines of C. annuum (‘S3586’ × ‘Kyoto-Manganji No. 2’). The map, designated as the SM-DH map, consisted of 15 linkage groups and the total map distance was 1403.8 cM. Mapping of quantitative trait loci (QTLs) for capsanthin content detected one QTL on linkage group (LG) 13 at 90 days after flowering (DAF) and one on LG 15 at 45 DAF; they were designated Cst13.1 and Cst15.1, respectively. Cst13.1 explained 17.0% of phenotypic variance and Cst15.1 explained 16.1%. We grouped DH lines according to the genotypes of markers adjacent to Cst13.1 and Cst15.1 on both sides. The DH lines with the alleles of both QTLs derived from ‘S3586’ showed higher capsanthin content at 45 and 90 DAF than the other lines. This is the first identification of QTLs for capsanthin content in any plant species. The data obtained here will be useful in marker-assisted selection for pepper breeding for high capsanthin content.
The brown planthopper (BPH) is a serious insect pest of rice and a substantial threat to rice production. Identification of new BPH resistance genes and their transfer into modern rice cultivars are effective breeding approaches to reduce the damage caused by BPH. In this study, we mapped a BPH resistance gene to a 50-kb genomic interval between two InDel markers 4M03980 and 4M04041 on the short arm of chromosome 4 in indica rice cultivar BP60, where the BPH resistance gene was mapped in Rathu Heenati by Liu et al. (2015) and named “Bph3”. This region contains two annotated genes Os04g0201900 and Os04g0202300, which encode lectin receptor kinases responsible for BPH resistance. We also developed a molecular marker “MM28T” for Bph3, and introgression Bph3 into susceptible rice restorer lines Guihui582 and Gui7571 by the marker-assisted selection (MAS) approach. The BPH resistance level is significantly enhanced in the Bph3-introgression lines, the resistance scores decrease from 8.2 to 3.6 for Guihui582 and decrease from 8.7 to around 3.8 for Gui7571. Therefore, developing molecular markers for the BPH resistance gene Bph3 and using them for molecular breeding will facilitate the creation of BPH-resistance rice cultivars to reduce damage caused by BPH.
Bacterial spot (caused by Xanthomonas arboricola pv. pruni) is a serious disease and difficult to control in peach cultivation, and inheritance manner of susceptibility is unclear. Five hundred and fourteen offspring and their parents from 27 peach full-sib families were evaluated for susceptibility to bacterial spot by evaluating lesion length value (LLV) after artificial inoculation to shoots from trees growing in the field. Brazilian cultivars including ‘Chimarrita’ and selections derived from them had notably lower LLVs ranging from 0.302 to 0.490 than those from Japanese cultivars/selections ranging from 0.514 to 1.295. Family means in offspring crossed between Brazilian cultivars/selections (low LLVs) and other cultivars/selections (high LLVs) showed rather low LLVs, whose values were close to Brazilian cultivar/selection parents. These results suggested that the susceptibility was controlled by single major gene and that the Brazilian and Japanese cultivar/selection parents showed dominant and recessive homozygotes, respectively. In contrast, the LLVs of family means were very high ranging from 0.719 to 1.194 in offspring population derived from crosses among Japanese cultivars. Repeated backcrosses of Brazilian cultivars/selections with Japanese cultivars/selections having high fruit quality are proposed as an effective method for developing new cultivars combining bacterial spot resistance and fruit quality in Japan.
Homeotic alteration phenotype of the flowers in Daucus carota are widely used for hybrid breeding, consequently molecular markers tightly-linked to such phenotype are in demand. Here we report the identification of a gene locus responsible for the phenotypic expression of stamen conversion into a petal-like structure, or petaloid. Using a segregating population and sequencing analysis of two bulked populations, we discovered a large contributing peak on the long arm of chromosome 4. DcMADS2, a homolog of the B-class floral homeotic gene PISTILLATA, found at the center of the peak region, was considered the strongest candidate causal gene. We established PCR primers that could be used to distinguish the two DcMADS2 alleles linked to each petaloid- and non-petaloid-phenotype.
Petunia (Petunia hybrida) is an important ornamental plant with a wide range of corolla colors. Although pale-yellow-flowered cultivars, with a low amount of carotenoids in their corollas, are now available, no deep-yellow-flowered cultivars exist. To find why petunia cannot accumulate enough carotenoids to have deep-yellow flowers, we compared carotenoid profiles and expression of carotenoid metabolic genes between pale-yellow-flowered petunia and deep-yellow-flowered calibrachoa (Calibrachoa hybrida), a close relative. The carotenoid contents and the ratios of esterified xanthophylls to total xanthophylls in petunia corollas were significantly lower than those in calibrachoa, despite similar carotenoid components. A lower esterification rate of trans-xanthophylls than of cis-xanthophylls in petunia suggests that petunia xanthophyll esterase (XES) has low substrate specificity for trans-xanthophylls, which are more abundant than cis-xanthophylls in petunia corolla. The expression of genes encoding key enzymes of carotenoid biosynthesis was lower and that of a carotenoid catabolic gene was higher in petunia. XES expression was significantly lower in petunia. The results suggest that low biosynthetic activity, high cleavage activity, and low esterification activity cause low carotenoid accumulation in petunia corollas.
Cryptomeria japonica is a major forestry tree species in Japan. Male sterility of the species is caused by a recessive gene, which shows dysfunction of pollen development and results in no dispersed pollen. Because the pollen of C. japonica induces pollinosis, breeding of pollen-free C. japonica is desired. In this study, single nucleotide polymorphism (SNP) markers located at 1.78 and 0.58 cM to a male sterility locus (MS1) were identified from an analysis of RNA-Seq and RAD-Seq, respectively. SNPs closely linked to MS1 were first scanned by a method similar to MutMap, where a type of index was calculated to measure the strength of the linkage between a marker sequence and MS1. Linkage analysis of selected SNP markers confirmed a higher efficiency of the current method to construct a partial map around MS1. Allele-specific PCR primer pair for the most closely linked SNP with MS1 was developed as a codominant marker, and visualization of the PCR products on an agarose gel enabled rapid screening of male sterile C. japonica. The allele-specific primers developed in this study would be useful for establishing the selection of male sterile C. japonica.
To understand variation in the root development traits (total root length (TRL), maximum root length (MRL) and root number) of 18 New Rice for Africa (NERICA) varieties, seedlings were hydroponically grown under deficient and sufficient concentrations of two forms of nitrogen, NH4+ and NO3–. The donor African rice variety, ‘CG14’ (Oryza glaberrima Steud.), showed greater TRL and MRL than three background Asian rice varieties (Oryza sativa L.). Wide distribution was observed in all traits of the 18 NERICAs. The 18 NERICAs and parental varieties were classified into three cluster groups by cluster analysis. Cluster Ia included only ‘CG14’. Comparative analysis characterized cluster Ib (including ‘NERICA7’) as an active root elongation group, and cluster II (including ‘WAB56-104’) as an active primordia development group. QTL analysis of F2 plants developed from a cross between ‘WAB56-104’ and ‘NERICA7’ detected two putative quantitative trait loci (QTLs) for root elongation on chromosome 1. Of these, a major QTL, designated as qRL1.4-NERICA7, was an NH4+-responsive QTL, which was narrowed down to a 0.7-Mbp region through progeny testing using F7 lines. qRL1.4-NERICA7 should help us understand genetic control in NERICAs, and improve root elongation in rice breeding programs.
Accurate evaluation of morphological and physiological traits is critical for selection of wheat (Triticum aestivum L.) cultivars exhibiting high yield, which is stable over different growing conditions. In order to use selection index based on high yield, high grain quality and drought tolerance in wheat, a set of 145 CIMMYT Wheat Physiological Germplasm Screening Nursery lines and seven local spring wheat varieties were phenotyped and evaluated for physiological and yield traits under two irrigation regimes during the 2011 and 2012 growing seasons in Xinjiang, China. The results showed that drought-stress significantly increased canopy temperature but reduced grain yield, grain weight per spike, normalized difference vegetation index at the flowering and grain filling stages, chlorophyll content at the grain filling stage, grain plumpness, grain number per spike, thousand-grain weight, and plant height. Grain weight per spike, plant height and grain plumpness explained 61.8% of the total phenotypic variation in grain yield under no-stress conditions, where they were the three principal factors most closely related to grain yield. Under drought-stress conditions, canopy temperature at the grain filling stage, plant height and grain plumpness were the three principal factors affecting grain yield, and contributed 44.8% of the total phenotypic variation in grain yield. Finally, ten genotypes, including three local varieties, ‘Xinchun 11’, ‘Xinchun 23’ and ‘Xinchun 29’, with appropriate plant height and high and stable yield under both no-stress and drought-stress conditions over the two years of trials, were identified and can be recommended as core parents for spring wheat drought tolerance breeding in Xinjiang, China.
The fungal pathogen Pyricularia oryzae causes blast, a severe disease of rice (Oryza sativa L.). Improving blast resistance is important in rice breeding programs. Inoculation tests have been used to select for resistance genotypes, with DNA marker-based selection becoming an efficient alternative. No comprehensive DNA marker system for race-specific resistance alleles in the Japanese rice breeding program has been developed because some loci contain multiple resistance alleles. Here, we used the Fluidigm SNP genotyping platform to determine a set of 96 single nucleotide polymorphism (SNP) markers for 10 loci with race-specific resistance. The markers were then used to evaluate the presence or absence of 24 resistance alleles in 369 cultivars; results were 93.5%consistent with reported inoculation test-based genotypes in japonica varieties. The evaluation system was successfully applied to high-yield varieties with indica genetic backgrounds. The system includes polymorphisms that distinguish the resistant alleles at the tightly linked Pita and Pita-2 loci, thereby confirming that all the tested cultivars with Pita-2 allele carry Pita allele. We also developed and validated insertion/deletion (InDel) markers for ten resistance loci. Combining SNP and InDel markers is an accurate and efficient strategy for selection for race-specific resistance to blast in breeding programs.
Seed coat color is an important agronomic trait in Brassica rapa. Yellow seeds are a desirable trait for breeding oilseed Brassica crops. To identify quantitative trait loci (QTLs) that condition seed coat color in B. rapa, we used a population of recombinant inbred lines (RILs) derived from crossing 09A001, a standard rapid-cycling (RcBr) inbred line of B. rapa L. ssp. dichotoma with yellow seeds, with 08A061, an inbred line of heading Chinese cabbage with dark brown seeds. Using two phenotypic scoring methods, we detected a total of nine QTLs distributed on four chromosomes (Chrs.), A03, A06, A08, and A09, that explained 3.17 to 55.73% of the phenotypic variation for seed color. To validate the effects of the identified QTLs in the RIL population, chromosome segment substitution lines (CSSLs) harboring the chromosomal segment carrying the candidate QTL region from 08A061 were selected, and two co-localized major QTLs, qSC9.1 and qSCb9.1, and one minor QTL, qSC3.1, were successfully validated. The validated QTL located on Chr. A03 appears to be a new locus underlying seed coat color in B. rapa. These findings provide additional insight that will help explain the complex genetic mechanisms underlying the seed coat color trait in B. rapa.