Human selection maintains karyotype integrity of highly unstable genomic cultivated autotetraploid potato (Solanum tuberosum)

Abstract

Understanding meiotic and genomic stability in polyploid species is critical for advancing genetic discovery and breeding. Potato (Solanum tuberosum), the third most important food crop globally, is represented by cultivated potato, an autotetraploid with highly heterozygous genomes. Here, we revealed that cultivated potato showed different chromosomal pairing configurations and irregular chromosomal segregations, resulting in a high proportion of aneuploid gametes. Aneuploidy was identified in inbreeding and outbreeding populations of cultivated potato, with frequencies ranging from 14.8 to 24.0%, indicating notable genomic instability. Extensive novel copy number variations (CNVs) were detected in the progeny, which may increase genetic diversity. Molecular karyotyping of 50 commercial varieties revealed that all varieties were euploid, with significantly fewer CNVs, indicating that human selection maintains karyotypic integrity. Aneuploids in the outbreeding population exhibited poor agronomic traits and fitness defects, which demonstrated that genomic instability increases phenotypic diversity. Our study provides insights into genetic basis and phenotypic plasticity of cultivated potato, offering guidance for future breeding strategies.

Fig. 1.. Chromosome pairing and segregation during meiosis in cultivated potato.

Individual potato chromosomes at diakinesis and anaphase I of PMCs are identified using oligo-FISH barcodes [(A) and (C)] followed by a second FISH using probes CL14 and CL34 [(B) and (D)]. (A) Chromosome pairing of Atlantic potato at diakinesis illustrated by oligo-FISH. Four copies of each of the 12 chromosomes exhibited variable pairing patterns, including quadrivalent (shown in green), trivalents (shown in yellow), bivalents (shown in white), and univalents (shown in pink). (B) The same cell in (A) was reprobed by FISH using CL14 (red) and CL34 (green). (C) Chromosome segregation at anaphase I of meiosis in Atlantic illustrated by oligo-FISH. Nondisjunction of homologous chromosome results migration of three copies of chromosome 6 to one daughter cell (red text). (D) The same cells in (C) were reprobed by FISH using CL14 (red) and CL34 (green). Scale bars, 10 μm.

Fig. 2.. Chromosome pairing configurations and chromosome number distributions at anaphase I of meiosis in cultivated potato.

(A) Chromosome pairing configurations at diakinesis. U univalent, B bivalent, T trivalent, Q quadrivalent. n = 52, 72, 70, and 72 nuclei for Atlantic, Kexin23, W2, and Menghuang2, respectively. (B) Chromosome number distributions at anaphase I. PS, premature sister chromatid separation; Lag, cells with lagging chromosome. n = 59, 45, 109, and 123 cells for Atlantic, Kexin23, W2, and Menghuang2, respectively. Data are presented as mean values ± SE.

Fig. 3.. Molecular karyotyping and oligo-FISH reveal chromosomal number variations in inbreeding and outbreeding populations of cultivated potato.

(A) Molecular karyotyping of the inbreeding line 2018-12-25 using bioinformatics methods. The scatter represents the ratio*4 (ploidy), whereas the black segments indicate the copy number of each chromosome. The red square indicates the presence of five copies of chromosome 3. (B) Chromosome identification via oligo-FISH confirms that the inbreeding line 2018-12-25 is aneuploid with 49 chromosomes. (C) Individual chromosomes from the same cell in (B) were excised and arranged on the basis of the number and positions of the red/green signals, confirming the additional copy of chromosome 3 (underlined). (D) Molecular karyotyping of the outbreeding line 2018-08-5 showed five copies of chromosome 3 (highlighted in a red square). (E) Oligo-FISH analysis reveals that the outbreeding line 2018-08-5 is aneuploid with 49 chromosomes. (F) Cytogenetic karyotyping by oligo-FISH verifies that the presence of five copies of chromosome 3 (underlined). Scale bars, 10 μm.

Fig. 4.. Estimations of CNVs in cultivated autotetraploid potato.

(A) Proportion of CNVs in Atlantic and its inbreeding population. n = 50 plants for At-S1. (B) Proportion of CNVs in variety C88 and its inbreeding population. n = 50 plants for C88-S1. (C) Proportion of overlapped CNVs (preexisting dosage variation) between Atlantic and its inbreeding population. n = 50 plants for At-S1. (D) Proportion of overlapped CNVs between variety C88 and its inbreeding population. n = 50 plants for C88-S1. (E) Comparison of the chromosomal distribution of novel and preexisting CNVs between the parental variety Atlantic and its derived inbreeding line. The top and bottom panels show the chromosomal distribution of CNVs in variety Atlantic and inbreeding line 202206-3, respectively. The scatter represents the ratio*4 (ploidy), and the black segments show the copy number of each chromosome. The copy number of the genome sequence deviating from four was counted as the CNVs. The middle panels show the distribution of CNVs by colored strips on different chromosomes with pink strips of variety Atlantic and blue strips of inbreeding line 202206-3, whereas purple indicates preexisting CNVs. (F) Proportion of CNVs in the inbreeding population (n = 50), outbreeding population (n = 50), and varieties of cultivated potato (n = 50). n.s., not significant.

Fig. 5.. Phenotypic variation in euploid and aneuploid offspring of cultivated potato.

(A) Euploid line 201803-2 exhibited a normal phenotype. (B to D and F to H) Six aneuploid lines displayed dwarf and early aging phenotypes. (B) Aneuploid line 201806-2. (C) Aneuploid line 201806-13. (D) Aneuploid line 201806-51. (E) Euploid line 201806-25 exhibited a fitness defect phenotype. (F) Aneuploid line 2018-07-24. (G) Aneuploid line 201807-52. (H) Aneuploid line 2018-08-5. (I to L) Comparison of agronomic phenotypes between euploid (n = 30) and aneuploid (n = 6) lines in the outbreeding population of cultivated potatoes. (I) Plant height. (J) Number of tubers per plant. (K) Yield per line. (L) Sensitivity to early blight. Data in (I) to (L) are presented as mean values ± SE. * indicates a statistically significant difference (P < 0.05); ** indicates a statistically significant difference (P < 0.01) using a Student’s t test.