Development of molecular inversion probes for soybean progeny genomic selection genotyping
Abstract Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome‐wide single‐nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Mole...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2023-03-01
|
| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20270 |
| _version_ | 1811154989438992384 |
|---|---|
| author | Haichuan Wang Benjamin Campbell Mary Happ Samantha McConaughy Aaron Lorenz Keenan Amundsen Qijian Song Vincent Pantalone David Hyten |
| author_facet | Haichuan Wang Benjamin Campbell Mary Happ Samantha McConaughy Aaron Lorenz Keenan Amundsen Qijian Song Vincent Pantalone David Hyten |
| author_sort | Haichuan Wang |
| collection | DOAJ |
| description | Abstract Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome‐wide single‐nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping‐by‐sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost‐effective, high‐throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern‐central and middle‐southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per‐sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs. |
| first_indexed | 2024-04-10T04:26:35Z |
| format | Article |
| id | doaj.art-baa7a91261b348bcbeee07ab4470f69c |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-04-10T04:26:35Z |
| publishDate | 2023-03-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-baa7a91261b348bcbeee07ab4470f69c2023-03-10T14:45:45ZengWileyThe Plant Genome1940-33722023-03-01161n/an/a10.1002/tpg2.20270Development of molecular inversion probes for soybean progeny genomic selection genotypingHaichuan Wang0Benjamin Campbell1Mary Happ2Samantha McConaughy3Aaron Lorenz4Keenan Amundsen5Qijian Song6Vincent Pantalone7David Hyten8Dep. of Agronomy and Horticulture Univ. of Nebraska–Lincoln Lincoln NE USADep. of Agronomy and Plant Genetics Univ. of Minnesota St. Paul MN USADep. of Agronomy and Horticulture Univ. of Nebraska–Lincoln Lincoln NE USADep. of Agronomy and Horticulture Univ. of Nebraska–Lincoln Lincoln NE USADep. of Agronomy and Plant Genetics Univ. of Minnesota St. Paul MN USADep. of Agronomy and Horticulture Univ. of Nebraska–Lincoln Lincoln NE USAUSDA–ARS, Soybean Genomics and Improvement Lab Beltsville MD USADep. of Plant Sciences Univ. of Tennessee Knoxville TN USADep. of Agronomy and Horticulture Univ. of Nebraska–Lincoln Lincoln NE USAAbstract Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome‐wide single‐nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping‐by‐sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost‐effective, high‐throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern‐central and middle‐southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per‐sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.https://doi.org/10.1002/tpg2.20270 |
| spellingShingle | Haichuan Wang Benjamin Campbell Mary Happ Samantha McConaughy Aaron Lorenz Keenan Amundsen Qijian Song Vincent Pantalone David Hyten Development of molecular inversion probes for soybean progeny genomic selection genotyping The Plant Genome |
| title | Development of molecular inversion probes for soybean progeny genomic selection genotyping |
| title_full | Development of molecular inversion probes for soybean progeny genomic selection genotyping |
| title_fullStr | Development of molecular inversion probes for soybean progeny genomic selection genotyping |
| title_full_unstemmed | Development of molecular inversion probes for soybean progeny genomic selection genotyping |
| title_short | Development of molecular inversion probes for soybean progeny genomic selection genotyping |
| title_sort | development of molecular inversion probes for soybean progeny genomic selection genotyping |
| url | https://doi.org/10.1002/tpg2.20270 |
| work_keys_str_mv | AT haichuanwang developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT benjamincampbell developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT maryhapp developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT samanthamcconaughy developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT aaronlorenz developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT keenanamundsen developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT qijiansong developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT vincentpantalone developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping AT davidhyten developmentofmolecularinversionprobesforsoybeanprogenygenomicselectiongenotyping |