Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection
Peas (<i>Pisum sativum</i>) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding pro...
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MDPI AG
2023-01-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/3/2470 |
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| author | Nicolas Rispail Osman Zakaria Wohor Salvador Osuna-Caballero Eleonora Barilli Diego Rubiales |
| author_facet | Nicolas Rispail Osman Zakaria Wohor Salvador Osuna-Caballero Eleonora Barilli Diego Rubiales |
| author_sort | Nicolas Rispail |
| collection | DOAJ |
| description | Peas (<i>Pisum sativum</i>) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD<sub>50</sub> distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of <i>Pisum</i> genus into two species, <i>P. fulvum</i> and <i>P. sativum</i> (including subsp. <i>sativum</i>, <i>arvense</i>, <i>elatius</i>, <i>humile</i>, <i>jomardii</i> and <i>abyssinicum</i>). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate <i>P. sativum</i> subsp. <i>jomardii</i> and <i>P. sativum</i> subsp. <i>arvense</i> during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches. |
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| language | English |
| last_indexed | 2024-03-11T09:40:59Z |
| publishDate | 2023-01-01 |
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| spelling | doaj.art-8851ea7cdfca49f1a369b21c94d1c9a32023-11-16T16:57:43ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01243247010.3390/ijms24032470Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core CollectionNicolas Rispail0Osman Zakaria Wohor1Salvador Osuna-Caballero2Eleonora Barilli3Diego Rubiales4Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, SpainInstituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, SpainInstituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, SpainInstituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, SpainInstituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, SpainPeas (<i>Pisum sativum</i>) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD<sub>50</sub> distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of <i>Pisum</i> genus into two species, <i>P. fulvum</i> and <i>P. sativum</i> (including subsp. <i>sativum</i>, <i>arvense</i>, <i>elatius</i>, <i>humile</i>, <i>jomardii</i> and <i>abyssinicum</i>). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate <i>P. sativum</i> subsp. <i>jomardii</i> and <i>P. sativum</i> subsp. <i>arvense</i> during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.https://www.mdpi.com/1422-0067/24/3/2470core collectionDArTSeqgenetic diversitygermplasmpeas<i>Pisum</i> spp. |
| spellingShingle | Nicolas Rispail Osman Zakaria Wohor Salvador Osuna-Caballero Eleonora Barilli Diego Rubiales Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection International Journal of Molecular Sciences core collection DArTSeq genetic diversity germplasm peas <i>Pisum</i> spp. |
| title | Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection |
| title_full | Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection |
| title_fullStr | Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection |
| title_full_unstemmed | Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection |
| title_short | Genetic Diversity and Population Structure of a Wide <i>Pisum</i> spp. Core Collection |
| title_sort | genetic diversity and population structure of a wide i pisum i spp core collection |
| topic | core collection DArTSeq genetic diversity germplasm peas <i>Pisum</i> spp. |
| url | https://www.mdpi.com/1422-0067/24/3/2470 |
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