Eastern black walnut (
As a step towards trait mapping in the halophyte seashore paspalum (
- NSF-PAR ID:
- 10153658
- Publisher / Repository:
- Nature Publishing Group
- Date Published:
- Journal Name:
- Scientific Reports
- Volume:
- 9
- Issue:
- 1
- ISSN:
- 2045-2322
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract Juglans nigra L.), one of the most valuable timber and veneer trees in North America, provides nut shells with unique industrial uses and nut kernels with distinctive culinary attributes. A mature F1full-sib progeny orchard of 248 individuals from the cross of two eastern black walnut cultivars provides a long-term resource for discovering genetic mechanisms controlling life history, quality traits, and stress resistance. The genetic linkage map, constructed with 356 single nucleotide polymorphism (SNP) markers and 62 expressed sequence tag simple sequence repeats (EST-SSRs), is 1645.7 cM in length, distributed across the expected 16 linkage groups. In this first application of QTL mapping inJ. nigra , we report QTL for budbreak, peak pistillate bloom, peak staminate bloom, and heterodichogamy. A dominant major QTL for heterodichogamy is reported, the sequence for which is syntenic with the heterodichogamy QTL on chromosome 11 of Persian walnut (J. regia L.). The mapping population parents are both protogynous, and segregation suggests a Mendelian component, with a 3:1-like inheritance pattern from heterozygous parents. Mapping the sequenced EST-SSR markers to theJ. regia “Chandler” V2.0 genome sequence revealed evidence for collinearity and structural changes on two of the sixteen chromosomes. The inclusion of sequenced EST-SSR markers enables the direct comparison of this and subsequentJ. nigra maps and otherJuglandaceae genetic maps. This investigation initiates long-term QTL detection studies for quality and stress resistance traits in black walnut. -
Abstract Wheat (
Triticum aestivum ) genetic maps are a key enabling tool for genetic studies. We used genotyping-by-sequencing-(GBS) derived markers to map recombinant inbred line (RIL) and doubled haploid (DH) populations from crosses of W7984 by Opata, and used the maps to explore features of recombination control. The RIL and DH populations, SynOpRIL and SynOpDH, were composed of 906 and 92 individuals, respectively. Two high-density genetic linkage framework maps were constructed of 2,842 and 2,961 cM, harboring 3,634 and 6,580 markers, respectively. Using imputation, we added 43,013 and 86,042 markers to the SynOpRIL and SynOpDH maps. We observed preferential recombination in telomeric regions and reduced recombination in pericentromeric regions. Recombination rates varied between subgenomes, with the D genomes of the two populations exhibiting the highest recombination rates of 0.26–0.27 cM/Mb. QTL mapping identified two additive and three epistatic loci associated with crossover number. Additionally, we used published POPSEQ data from SynOpDH to explore the structural variation in W7984 and Opata. We found that chromosome 5AS is missing from W7984. We also found 2,332 variations larger than 100 kb. Structural variants were more abundant in distal regions, and overlapped 9,196 genes. The two maps provide a resource for trait mapping and genomic-assisted breeding. -
Registration of two rice mapping populations using weedy rice ecotypes as a novel germplasm resource
Abstract Two mapping populations were developed from crosses of the Asian
indica rice (Oryza sativa L.) cultivar ‘Dee Geo Woo Gen’ (DGWG; PI 699210 Parent, PI 699212 Parent) and two weedy rice ecotypes, an early‐flowering straw hull (SH) biotype AR‐2000‐1135‐01 (PI 699209 Parent) collected in Arkansas and a late‐flowering black hull (BHA) biotype MS‐1996‐9 (PI 699211 Parent) collected in Mississippi. The weed and crop‐based rice recombinant inbred line (RIL) mapping populations have been used to identify genomic regions associated with weedy traits as well as resistance to sheath blight and rice blast diseases. The mapping population consists of 185 (DGWG/SH; Reg. no. MP‐9, NSL 541035 MAP) and 234 (BHA/DGWG; Reg. no. MP‐10, NSL 541036 MAP) F8RILs, of which 175 (DGWG/SH) and 224 (BHA/DGWG) were used to construct two linkage maps using single nucleotide polymorphic markers to identify weedy traits, sheath blight, and blast resistance loci. These mapping populations and related datasets represent a valuable resource for basic rice evolutionary genomic research and applied marker‐assisted breeding efforts in disease resistance. -
Abstract The first high-resolution genetic linkage map of the ancestral octoploid (2n = 8x = 56) strawberry species,
Fragaria virginiana , was constructed using segregation data obtained from a pentaploid progeny population. This novel mapping population of size 178 was generated by crossing highly heterozygousF. virginiana hybrid “LB48” as a paternal parent with diploid (2n = 2x = 14)Fragaria vesca “Hawaii 4”. The LB48 linkage map comprises 6055 markers genotyped on the Axiom® IStraw90 strawberry SNP array. The map consists of 28 linkage groups (LGs) organized into seven homoeology groups of four LGs each, and excludes a small 29th LG of undefined homoeology. One member of each homoeology group was assignable to an “A” subgenome associated with ancestral diploidFragaria vesca , while no other subgenomes were defined. Despite an intriguing discrepancy within homoeology group VI, synteny comparisons with the previously publishedFragaria ×ananassa DA × MO linkage map revealed substantial agreement. Following initial map construction, examination of crossover distributions revealed that six of the total 5162 (=29 chromosomes/individual × 178 individuals) chromosomes making up the data set exhibited abnormally high crossover counts, ranging from 15 to 48 crossovers per chromosome, as compared with the overall mean of 0.66 crossovers per chromosome. Each of these six hyper-recombinant (HypR) chromosomes occurred in a different LG and in a different individual. When calculated upon exclusion of the six HypR chromosomes, the canonical (i.e., broadly representative) LB48 map had 1851 loci distributed over a total map length of 1873 cM, while their inclusion increased the number of loci by 130, and the overall map length by 91 cM. Discovery of these hyper-recombinant chromosomes points to the existence of a sporadically acting mechanism that, if identified and manipulable, could be usefully harnessed for multiple purposes by geneticists and breeders. -
SUMMARY Sorghum anthracnose caused by the fungus
Colletotrichum sublineola (Cs ) is a damaging disease of the crop. Here, we describe the identification ofANTHRACNOSE RESISTANCE GENES (ARG4 andARG5 ) encoding canonical nucleotide‐binding leucine‐rich repeat (NLR) receptors.ARG4 andARG5 are dominant resistance genes identified in the sorghum lines SAP135 and P9830, respectively, that show broad‐spectrum resistance toCs . Independent genetic studies using populations generated by crossing SAP135 and P9830 with TAM428, fine mapping using molecular markers, comparative genomics and gene expression studies determined thatARG4 andARG5 are resistance genes againstCs strains. Interestingly,ARG4 andARG5 are both located within clusters of duplicate NLR genes at linked loci separated by ~1 Mb genomic region. SAP135 and P9830 each carry only one of theARG genes while having the recessive allele at the second locus. Only two copies of theARG5 candidate genes were present in the resistant P9830 line while five non‐functional copies were identified in the susceptible line. The resistant parents and their recombinant inbred lines carrying eitherARG4 orARG5 are resistant to strains Csgl1 and Csgrg suggesting that these genes have overlapping specificities. The role ofARG4 andARG5 in resistance was validated through sorghum lines carrying independent recessive alleles that show increased susceptibility.ARG4 andARG5 are located within complex loci displaying interesting haplotype structures and copy number variation that may have resulted from duplication. Overall, the identification of anthracnose resistance genes with unique haplotype stucture provides a foundation for genetic studies and resistance breeding.