Molecular Breeding

Hd1 function conversion in regulating heading is dependent on gene combinations of Ghd7 , Ghd8 , and Ghd7.1 under long-day conditions in rice Abstract Ghd7, Ghd8, Ghd7.1, and Hd1 are all pleiotropic genes regulating heading date, plant height, and yield in rice. Early studies showed that Hd1 promoted heading under short-day conditions (SD) and delayed heading under long-day conditions (LD). Recent studies found that Hd1 also promoted heading in some genetic backgrounds under LD. In this study, we developed a series of near-isogenic lines for Ghd7, Ghd8, Ghd7.1, and Hd1 in the Zhenshan 97 (ZS97) and Minghui 63 (MH63) backgrounds and recorded their heading dates. In the ZS97 background, Ghd7 alone triggered the conversion of Hd1 function from promoting to suppressing heading under LD. Ghd8 alone and Ghd7.1 alone did not promote but enhanced Ghd7-mediated Hd1 function conversion. In the MH63 background, Ghd7 alone and Ghd7.1 alone did not convert Hd1 function under LD, but they jointly promoted Hd1 function conversion. Conversion of Hd1 function occurred only under LD but not SD. Transcript analysis showed that downregulation or upregulation of Ehd1 and Hd3a by Hd1 in the lines under LD was determined by genetic background. In summary, multiple gene combinations of Ghd7, Ghd7.1, and Ghd8 and unknown genes caused conversion of Hd1 function. Moreover, the different gene combinations had a big difference in photoperiod sensitivities. These findings lay a solid foundation for further unveiling the molecular mechanism of Hd1 function conversion and provide guidance for heading date improvement in rice.

Identification of quantitative trait loci contributing resistance to aflatoxin accumulation in maize inbred Mp715 Abstract Aflatoxin is a mycotoxin produced by the fungus Aspergillus flavus (Link:Fr), an opportunistic ear-rot pathogen of maize (Zea mays L. ssp. mays). Pre-harvest contamination of maize grain with aflatoxin is a chronic problem worldwide and particularly in the Southeastern US. Quantitative trait loci (QTL) were mapped by multiple interval mapping (MIM) in a population consisting of 250 F2:3 lines derived from the cross Mp715 × Va35. Mp715 is resistant to the accumulation of aflatoxin and Va35 is susceptible. The population was genotyped with 1200 single-nucleotide polymorphism (SNP) and simple sequence repeat (SSR) molecular markers and phenotyped for the accumulation of total aflatoxins under artificial inoculation in four environments. Both parents contributed resistance alleles. Two QTL in bins 6.06 and 7.03 were the most promising for the marker-assisted introgression of the resistance present in Mp715. They were the most consistent across individual environments and together were responsible for nearly 30% of the phenotypic variance when data was combined across all four environments. In addition to those two QTL, Mp715 was also the source of the beneficial aflatoxin-reducing allele for several smaller effect QTL. Once their effect is validated in further experiments, the identification of these relatively large effect QTL should facilitate the utilization of this aflatoxin accumulation-resistant germplasm in applied maize breeding programs.

A user-friendly KASP molecular marker developed for the DGMS-based breeding system in Brassica oleracea species Abstract Cabbage 79-399-3 is a spontaneous male-sterile mutant controlled by the dominant genic gene (DGMS) Ms-cd1. Dozens of DGMS lines in cabbage, broccoli, kohlrabi, and Chinese kale have been created using 79-399-3 as a donor. To realize fast and accurate marker-assisted selection (MAS) and build a high-efficiency breeding system based on DMGS, a high-throughput, user-friendly marker is needed. In this study, we resequenced the DGMS line DGMS01-20 (backcross lines with over 20 generations) and its maintainer line 01-20 and developed four markers linked to Ms-cd1 using a segregating population of DGMS01-20. Kompetitive allele specific PCR (KASP) markers K13 and K23 were the flanking markers with genetic distances of 0.76 cM and 1.09 cM, respectively. K6 cosegregated with Ms-cd1 in all 919 individuals of the population. K13 and K6 were tested for their accuracy and applicability using 18 different DGMS lines. K13 was not applicable in five broccoli, kohlrabi, and Chinese kale DGMS lines, resulting in 72.2% accuracy, whereas K6 showed 100% accuracy in these DGMS lines and in an additional assessment using 35 inbred lines. Moreover, K6 can be used to genotype the self-pollination progenies of heterozygous plants (heterozygous means one Ms-cd1 allele and one wild-type allele; such plants produce pollen grains in very rare cases). The results showed that K6 is a reliable marker for accurately and rapidly identifying Ms-cd1 loci in Brassica oleracea; thus, it is beneficial for the DGMS-based breeding program in B. oleracea.

Genetic distance and the relationship with heterosis and reproductive behavior in tetraploid bahiagrass hybrids Abstract Bahiagrass (Paspalum notatum Flüggé) is one of the main components of the South American grasslands, and it is cultivated for forage and turf around the world. At present, hybridization is the most common breeding technique for the species, and its goal is to obtain superior apomictic hybrids. The objective of the present study was to determine the relationship between heterosis, reproductive behavior, and genetic distances between parents in tetraploid bahiagrass. Genetic distance between 24 sexual tetraploid genotypes and 24 apomictic tetraploid genotypes of P. notatum was evaluated using simple sequence repeat (SSR) and inter simple sequence repeat (ISSR) markers. Crosses were made between parents with low, intermediate, or high genetic distances. Six families were generated. A marker linked to apospory in bahiagrass was used to determine segregation for mode of reproduction, and embryo sacs were characterized to estimate the level of apospory expressivity. The ratio between sexual and aposporous hybrids ranged from 1:1 to 9:1 among families. Discontinuous variation for apospory expressivity was observed among hybrids, with either low or high levels being exhibited. A significant relationship between genetic distance and proportion of aposporous hybrids was observed. Heterosis was observed for all the evaluated traits and its level was dependent on the parental combination. Genetic distances between parents were related to heterosis, mainly for forage yield, which is the most important trait in forage species. Hence, molecular markers may be useful to predict the occurrence of heterosis for this trait.

Correction to: Improvement of seedling and panicle blast resistance in Xian rice varieties following Pish introgression The original article unfortunately contains an incorrect grant number in the funding information.

Integrating GWAS, QTL, mapping and RNA-seq to identify candidate genes for seed vigor in rice ( Oryza sativa L.) Abstract Seed vigor is an important seed quality trait in rice (Oryza sativa L.) that profoundly affects seedling morphogenesis in different environments. Generally, highly vigorous seeds have many advantages in agricultural production, such as resistance to adverse stresses, rapid emergence, and yield improvement. In the present study, one germplasm collection and one recombinant inbred line (RIL) population were used to identify quantitative trait loci (QTLs) for seed vigor. A total of 19 single nucleotide polymorphisms (SNPs) were found to be significantly associated with seed vigor (−log10(P) > 6) in the germplasm collection, which consisted of 200 rice cultivars. Nine loci responsible for seed vigor were identified via QTL mapping by using a high-density bin map. To screen the candidate genes more efficiently, we selected six loci that were co-localized in GWAS and QTL mapping, overlapped previous reports, repeat detected across two seasons, or high contribution rate as reliable loci. A total of 44 differentially expressed genes were obtained from the reliable loci via gene expression profile analysis. Among these 44 genes, Os06g0108600, Os06g0110200, Os06g0253100, Os06g0282000, Os07g0583600, Os07g0592600, and Os09g0432300 were the most promising candidates associated with seed vigor.

Genome-wide identification of silique-related traits based on high-density genetic linkage map in Brassica napus Abstract The yield of rapeseed is directly and indirectly influenced by silique-related traits, the genetic dissection, and improvement of the silique-related traits are thus the most important research project in rapeseed. Seven silique-related traits, including seed number per silique (SPS), silique length (SL), silique width (SW), silique thickness (ST), silique volume (SV), silique density (SD), and thousand seed weight (TSW) were further analyzed through quantitative trait locus (QTL) mapping based on a high-density genetic linkage map in KN population. A total of 273 identified QTLs were integrated into 230 consensus QTLs, in which 84.78% of consensus QTLs were considered to be environment-specific QTLs and 15.22% of consensus QTLs were considered to be environmentally stable expression QTLs. Two major QTLs, including cqSW.C6-5 for SW and cqSPS.C6-3 for SPS were identified on C06. According to QTLs integrated from different silique traits, 48 unique QTLs were identified with pleiotropy that involved in 2–5 silique-related traits. In addition, 185 epistatic locus pairs were identified with the PV ranging from 0.96 to 15.98%. QTL comparison were made between the KN population and other mapping populations, a total of 164 QTLs for silique-related traits (48 for SPS, 31 for SL, 7 for SD, and 78 for TSW) from nine previously reported researches were aligned to the Brassica napus reference genome, in which 23 QTLs were considered as new QTLs (8 for SD, 4 for SL, 7 for SPS, 4 for TSW). More importantly, cqSPS.C6-3 for SPS might be a novel major QTL. Furthermore, 82 candidate genes in B. napus corresponding to 48 candidate genes in Arabidopsis thaliana were identified, which were involved in transcription factors, enzymes, protein structure units, phytohormone response factors, and transporters, etc. These findings not only provided more comprehensive insights into the genetic basis for silique-related traits but also new cues for improving silique and increasing seed yield in B. napus.

Pyramiding of rapid germination loci from Oryza Sativa cultivar 'Xieqingzao B' and cold tolerance loci from Dongxiang wild rice to increase climate resilience of cultivated rice Abstract Rapid and uniform germination of seeds and subsequent high survivability of seedlings in low-temperature environments are two key requirements in the direct-seeding agronomic production system in rice. Dongxiang wild rice (DXWR), the northernmost common wild rice, possesses a number of seedling cold-tolerance loci and is an invaluable genetic resource for the molecular breeding of cold-tolerant rice. However, DXWR has a delayed and desynchronized germination trait in low-temperature environments that is favorable for its adaption to cold environments but is a disadvantage for seedling establishment in the direct-seeding system when integrated into elite cultivars. In the present study, we identified five quantitative trait loci (QTLs) for low-temperature germination in DXWR. All the DXWR alleles delay the germination of DXWR seeds in low-temperature environments. By the pyramiding of QTLs of rapid germination from cultivated rice and QTLs of seedling cold tolerance from high tolerance wild rice DXWR, we obtained a variety numbered DX71 with rapid and uniform germination of seeds and high cold tolerance of seedlings in low-temperature environments. The results could facilitate the understanding of the genetic basis of delayed germination in DXWR, partly explaining how DXWR adapts to low temperatures in its habitat. The identified QTLs provide tightly linked markers for rice breeding in the development of climate-resilient varieties with low input.

Introgressing the allelic variation of a major locus in reducing the grain cadmium accumulation in indica rice hybrids Abstract Cadmium (Cd) is a toxic element that can accumulate in rice grains, presenting a threat to human health. Indica rice hybrid is dominant in southern China, and this genetic background is linked to high-level Cd accumulation in grains. Thus, lowering grain Cd levels in indica hybrids is a priority in the breeding programs. Previously, a locus on chromosome 7 was found to be associated with grain Cd variation in 617 rice hybrids and exhibited apparent indica–japonica differentiation. In this present study, a backcross population was generated to investigate the genetic control of this locus, as qCd7, on grain Cd performance in rice. Quantitative trait locus (QTL) analysis revealed qCd7 as an incomplete dominant factor that has a major effect on grain Cd variation; the 'NPB' allele can reduce grain Cd content. Using a 3 × 13 NCII design population, we evaluated qCd7's potential to decrease grain Cd content in indica hybrid combinations, and phenotypic comparisons indicated that introgression of qCd7-NPB effectively reduced grain Cd accumulation. Combining ability analysis revealed that parental lines carrying qCd7-NPB consistently displayed negative general combination ability (GCA) effects on grain Cd accumulation, which could be used to predict stable combiners in breeding programs. These results suggest that introgression of qCd7-NPB has great potential to decrease grain Cd content in indica hybrid breeding, which suggested that identifying allelic variation derived from indica–japonica genetic differences could facilitate genetic improvement in low grain Cd indica hybrid breeding programs.

Combining genome-wide linkage mapping with extreme pool genotyping for stripe rust resistance gene identification in bread wheat Abstract Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important diseases of wheat (Triticum aestivum) in China and is responsible for major production losses worldwide. Wheat cultivar Centrum was resistant at seedling stage to Chinese Pst isolate V26-10. To map the gene(s) conferring resistance, Centrum was crossed with the susceptible cultivar MX169. Genetic analysis of F1, F2, F2:3, and F2:6 populations showed that resistance was conferred by a single recessive gene, tentatively named Yrcen. The F2:6 population was genotyped using Illumina 35 K SNP (single nucleotide polymorphism) assays. Gene Yrcen was located on chromosome 1DS. To saturate the genetic map, the Affymetrix Wheat 660 K SNP array was used to screen bulked extreme phenotype DNA pools. Eight SNPs were located around the resistance gene. After combining SNP data from both the 35 K and 660 K assays, Yrcen was mapped to an interval of 1.7 cM flanked by markers AX-94530296 and AX-94434109. These two markers were validated for marker assisted selection of Yrcenusing a panel of 96 wheat cultivars and breeding lines. These tightly linked markers will be useful in developing cultivars for resistance to stripe rust.

Alexandros Sfakianakis
Anapafseos 5 . Agios Nikolaos
Crete.Greece.72100
2841026182

6948891480

alsfakia@gmail.com