Key messageUsing a combination of phenotypic screening, genetic and statistical analyses, and high-throughput genome-wide sequencing, we have finely mapped a dominant Phytophthora resistance gene in soybean cultivar Wayao.Abstract Phytophthora root rot (PRR) caused by Phytophthora sojae is one of the most important soil-borne diseases in many soybean-production regions in the world. Identification of resistant gene(s) and incorporating them into elite varieties are an effective way for breeding to prevent soybean from being harmed by this disease. Two soybean populations of 191 F2 individuals and 196 F7:8 recombinant inbred lines (RILs) were developed to map Rps gene by crossing a susceptible cultivar Huachun 2 with the resistant cultivar Wayao. Genetic analysis of the F2 population indicated that PRR resistance in Wayao was controlled by a single dominant gene, temporarily named RpsWY, which was mapped on chromosome 3. A high-density genetic linkage bin map was constructed using 3469 recombination bins of the RILs to explore the candidate genes by the high-throughput genome-wide sequencing. The results of genotypic analysis showed that the RpsWY gene was located in bin 401 between 4466230 and 4502773 bp on chromosome 3 through line 71 and 100 of the RILs. Four predicted genes (Glyma03g04350, Glyma03g04360, Glyma03g04370, and Glyma03g04380) were found at the narrowed region of 36.5 kb in bin 401. These results suggest that the high-throughput genome-wide resequencing is an effective method to fine map PRR candidate genes.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2869-5) contains supplementary material, which is available to authorized users.
Medicago polymorpha is a nutritious and palatable forage and vegetable plant that also fixes nitrogen. Here, we reveal the chromosome-scale genome sequence of M. polymorpha using an integrated approach including Illumina, PacBio and Hi-C technologies. We combined PacBio full-length RNA-seq, metabolomic analysis, structural anatomy analysis and related physiological indexes to elucidate the important agronomic traits of M. polymorpha for forage and vegetable usage. The assembled M. polymorpha genome consisted of 457.53 Mb with a long scaffold N50 of 57.72 Mb, and 92.92% (441.83 Mb) of the assembly was assigned to seven pseudochromosomes. Comparative genomic analysis revealed that expansion and contraction of the photosynthesis and lignin biosynthetic gene families, respectively, led to enhancement of nutritious compounds and reduced lignin biosynthesis in M. polymorpha. In addition, we found that several positively selected nitrogen metabolism-related genes were responsible for crude protein biosynthesis. Notably, the metabolomic results revealed that a large number of flavonoids, vitamins, alkaloids, and terpenoids were enriched in M. polymorpha. These results imply that the decreased lignin content but relatively high nutrient content of M. polymorpha enhance its edibility and nutritional value as a forage and vegetable. Our genomic data provide a genetic basis that will accelerate functional genomic and breeding research on M. polymorpha as well as other Medicago and legume plants.
The effects of neutral salt and alkali on the ion distribution were investigated in two alfalfa (Medicago sativa L.) cultivars, including Zhongmu 1, a high salt-tolerant cultivar, and Algonquin, a low salt-tolerant cultivar. The alkali stress expressed more serious growth inhibition than the neutral salt stress at the same Na + concentration. Compared with Algonquin, Zhongmu 1 did not exhibit a higher alkali tolerance under the Na 2 CO 3 -NaHCO 3 treatment with the low Na + concentration (50 mmol L -1 ). The alkali increased the accumulation of Na + , Ca 2+ , and Mg 2+ in the root and changed the Ca 2+ and Mg 2+ balance in the entire alfalfa plant. The salt and alkali stresses decreased the K + and Fe 3+ contents of the roots and leaves, the root Mn 2+ content, and the shoot Zn 2+ content, but they increased the Fe 3+ accumulation of the shoots, the shoot and leaf Cu 2+ contents, and the leaf Zn 2+ content in both alfalfa cultivars. Based on the results obtained under the conditions of this experiment, we found that the salt and alkali stresses reduced the plant growth in both alfalfa cultivars, while the alkali caused a stronger stress than the neutral salt in alfalfa. Thus, we conclude that under hydroponic conditions, the deleterious effects of the alkali on plants are due to the distribution change of some trophic ion balance in the roots, shoots, and leaves of the plants by causing of Na + , CO 3 2-, and/or HCO 3 stresses.
Bohai Black (BHB) cattle, one of eight representative indigenous breeds in China, is well known for its high resistance to disease, endurance under unfavorable feeding conditions and excellent meat quality. Over recent, the number of BHB cattle has decreased sharply. To investigate the population structure and genetic diversity of this breed, the whole-genome data of 35 individuals from a conservation farm were obtained using the Illumina 150 bp paired-end platform. The results of the genetic structure and diversity analyses showed that BHB cattle had mixed Bos taurus and Bos indicus ancestry, close phylogenic relationships with Jiaxian Red and Luxi cattle and abundant genetic diversity. The bulls tested here could be divided into six families. This study presents a comprehensive evaluation of the genetic structure and diversity of the BHB cattle, and lays the theoretical basis for conservation and utilization of the valuable germplasm resource.
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