Genetic Diversity and Population Structure in Solanum nigrum Based on Single-Nucleotide Polymorphism (SNP) Markers
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Materials
2.2. Genomic DNA Extractions and Specific-Locus Amplified Fragment Sequencing
2.3. Sequence Alignment for SNP Calling and Quality Assessment
2.4. Genetic Differentiation Analyses
2.5. Phylogenetic Analysis
3. Results
3.1. Phylogenetic Analyses on S. nigrum Populations
3.2. Genetic Differences and Genetic Distances of S. nigrum
3.3. Population Structure of S. nigrum
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
ID | Biogeographic Regions | Longitude | Latitude | ID | Biogeographic Regions | Longitude | Latitude |
---|---|---|---|---|---|---|---|
SB1 | Bei**g | 116°16′45″ | 39°33′16″ | SX15 | **njiang | 85°63′07″ | 44°19′31″ |
SH1 | Heilongjiang | 122°77′19″ | 52°22′92″ | SX16 | **njiang | 86°50′25″ | 44°23′50″ |
SH2 | Heilongjiang | 133°52′53″ | 47°24′19″ | SX17 | **njiang | 84°58′38″ | 44°34′17″ |
SH3 | Heilongjiang | 124°54′42″ | 47°08′55″ | SX18 | **njiang | 86°50′25″ | 44°23′50″ |
SH4 | Heilongjiang | 124°28′01″ | 47°45′39″ | SX19 | **njiang | 85°0′12″ | 44°27′45″ |
SJ1 | Jilin | 123°43′53″ | 44°10′83″ | SX20 | **njiang | 86°37′30″ | 44°28′59″ |
SJ2 | Jilin | 124°1′57″ | 44°17′20″ | SX21 | **njiang | 81°40′59″ | 45°0′14″ |
SJ3 | Jilin | 122° 55′82″ | 45°07′49″ | SX22 | **njiang | 86°24′17″ | 44°30′58″ |
SJ4 | Jilin | 122°54′14″ | 44°36′12″ | SX23 | **njiang | 85°1′36″ | 44°31′37 |
SJ5 | Jilin | 123°55′52″ | 44°17′31″ | SX24 | **njiang | 80°54′50″ | 40°34′57″ |
SJ6 | Jilin | 123°46′35″ | 44°13′60″ | SX25 | **njiang | 81°18′6″ | 40°32′37″ |
SJ7 | Jilin | 123°48′56″ | 44°41′54″ | SX26 | **njiang | 89°08′31″ | 42°57′14″ |
SL1 | Liaoning | 120°50′50″ | 40°44′18″ | SX27 | **njiang | 86°33′85″ | 46°19′43″ |
SL2 | Liaoning | 120°52′35″ | 40°46′51″ | SX28 | **njiang | 85°42′23″ | 46°05′11″ |
SM1 | Inner Mongolia | 121°19′52″ | 43°45′52″ | SX29 | **njiang | 84°43′12″ | 45°25′26″ |
SM2 | Inner Mongolia | 121°19′52″ | 43°45′52″ | SX31 | **njiang | 84°37′17″ | 44°32′21″ |
SN1 | Henan | 113°41′44″ | 35°15′32″ | SX32 | **njiang | 84°58′38″ | 44°34′17 |
SN2 | Henan | 114°55′22″ | 34°51′59″ | SX33 | **njiang | 82°06′20″ | 44°58′02″ |
SS1 | Shaanxi | 108°13′57″ | 34°23′38″ | SX34 | **njiang | 85°36′49″ | 48°08′38″ |
SX02 | **njiang | 81°32′6″ | 45°5′12″ | SX35 | **njiang | 84°59′56″ | 44°25′45″ |
SX03 | **njiang | 86°24′17″ | 44°30′58″ | SX36 | **njiang | 86°37′30″ | 44°28′59″ |
SX04 | **njiang | 82°20′33″ | 44°51′60″ | SX37 | **njiang | 85°51′54″ | 47°32′53″ |
SX05 | **njiang | 86°51′46″ | 44°20′28″ | SX38 | **njiang | 88°01′57″ | 47°14′16″ |
SX06 | **njiang | 82°24′30″ | 44°49′48″ | SX39 | **njiang | 87°58′31″ | 47°18′39″ |
SX07 | **njiang | 86°37′30″ | 44°28′59″ | SX40 | **njiang | 87°12′18″ | 44°07′12″ |
SX08 | **njiang | 82°10′35″ | 44°37′59″ | SX41 | **njiang | 87°04′44″ | 42°15′58″ |
SX09 | **njiang | 82°27′7″ | 44°37′51″ | SX42 | **njiang | 88°1′52 “ | 47°14′16 “ |
SX01 | **njiang | 82°5′43″ | 44°39′25″ | SX43 | **njiang | 86°48′07″ | 40°10′06″ |
SX10 | **njiang | 82°6′22″ | 44°53′2″ | SX44 | **njiang | 87°12′18″ | 44°07′12″ |
SX11 | **njiang | 82°8′60″ | 44°39′1″ | SX45 | **njiang | 87°04′44″ | 42°15′58″ |
SX12 | **njiang | 85°48′55″ | 41°43′36″ | SX46 | **njiang | 88°01′57″ | 47°14′16″ |
SX13 | **njiang | 84°58′38″ | 44°34′17″ | SX47 | **njiang | 87°15′06″ | 44°08′31″ |
SX14 | **njiang | 86°50′25″ | 44°23′50″ | SX48 | **njiang | 85°06′37″ | 44°19′03″ |
ID | Total Reads | GC Percentage (%) | Q30 Percentage (%) | ID | Total Reads | GC Percentage (%) | Q30 Percentage (%) |
---|---|---|---|---|---|---|---|
SB1 | 1,691,734 | 42.73 | 93.84 | SX15 | 1,650,570 | 43.41 | 94.14 |
SH1 | 1,807,444 | 42.05 | 94.47 | SX16 | 1,519,690 | 43.44 | 94.39 |
SH2 | 1,902,574 | 42.80 | 94.42 | SX17 | 1,737,036 | 42.87 | 93.68 |
SH3 | 1,823,795 | 43.30 | 94.01 | SX18 | 2,002,105 | 43.27 | 94.15 |
SH4 | 1,716,365 | 43.0 | 93.65 | SX19 | 1,736,208 | 43.40 | 94.31 |
SJ1 | 2,662,305 | 42.15 | 94.57 | SX20 | 1,681,088 | 43.44 | 94.47 |
SJ2 | 1,494,444 | 42.98 | 94.02 | SX21 | 1,622,367 | 43.09 | 94.48 |
SJ3 | 1,735,455 | 43.30 | 94.68 | SX22 | 1,598,613 | 43.41 | 94.58 |
SJ4 | 3,858,231 | 42.72 | 94.36 | SX23 | 1,534,640 | 43.47 | 94.78 |
SJ5 | 1,643,277 | 43.10 | 93.62 | SX24 | 1,941,331 | 43.02 | 94.58 |
SJ6 | 2,131,241 | 43.27 | 94.01 | SX25 | 2,100,514 | 42.83 | 94.29 |
SJ7 | 1,588,142 | 42.71 | 93.70 | SX26 | 1,716,587 | 42.76 | 94.53 |
SL1 | 1,883,192 | 43.04 | 94.02 | SX27 | 1,896,964 | 43.15 | 93.89 |
SL2 | 1,616,090 | 43.44 | 94.53 | SX28 | 2,049,341 | 43.24 | 94.14 |
SM1 | 1,657,653 | 42.95 | 94.42 | SX29 | 1,799,983 | 43.29 | 93.80 |
SM2 | 2,166,560 | 42.33 | 93.63 | SX31 | 1,812,148 | 42.8 | 93.90 |
SN1 | 2,109,751 | 42.85 | 93.91 | SX32 | 1,838,587 | 42.82 | 93.44 |
SN2 | 1,676,914 | 43.00 | 94.43 | SX33 | 1,753,477 | 43.08 | 94.06 |
SS1 | 1,620,348 | 42.88 | 94.09 | SX34 | 1,769,883 | 43.0 | 94.23 |
SX01 | 2,450,367 | 41.97 | 94.76 | SX35 | 1,712,473 | 43.29 | 94.27 |
SX02 | 1,723,640 | 42.68 | 93.92 | SX36 | 1,522,925 | 42.49 | 93.27 |
SX03 | 2,213,391 | 41.92 | 94.75 | SX37 | 1,731,599 | 42.72 | 93.57 |
SX04 | 1,973,084 | 42.03 | 94.79 | SX38 | 1,711,985 | 42.73 | 93.68 |
SX05 | 1,958,204 | 42.30 | 94.77 | SX39 | 1,789,567 | 42.51 | 93.37 |
SX06 | 2,121,610 | 42.05 | 94.63 | SX40 | 1,442,651 | 42.36 | 93.34 |
SX07 | 2,053,106 | 42.13 | 94.73 | SX41 | 1,563,989 | 42.78 | 93.21 |
SX08 | 2,393,941 | 41.88 | 94.58 | SX42 | 1,527,690 | 42.56 | 93.11 |
SX09 | 2,205,426 | 42.09 | 94.63 | SX43 | 1,741,900 | 42.61 | 93.55 |
SX10 | 2,023,837 | 42.51 | 94.57 | SX44 | 1,974,449 | 42.57 | 93.60 |
SX11 | 2,404,368 | 42.03 | 94.49 | SX45 | 1,895,990 | 42.50 | 93.53 |
SX12 | 1,750,841 | 42.12 | 94.55 | SX46 | 1,606,552 | 42.57 | 93.42 |
SX13 | 1,863,520 | 42.87 | 94.41 | SX47 | 1,823,353 | 42.65 | 93.87 |
SX14 | 1,451,126 | 43.35 | 94.15 | SX48 | 1,546,745 | 42.65 | 93.81 |
ID | SLAF Number | Total Depth | Average Depth | ID | SLAF Number | Total Depth | Average Depth |
---|---|---|---|---|---|---|---|
SB1 | 143,008 | 1,397,095 | 9.77 | SX15 | 143,551 | 1,201,101 | 8.37 |
SH1 | 139,623 | 1,558,808 | 11.16 | SX16 | 142,910 | 1,182,897 | 8.28 |
SH2 | 150,756 | 1,514,661 | 10.05 | SX17 | 135,530 | 1,473,942 | 10.88 |
SH3 | 148,052 | 1,447,856 | 9.78 | SX18 | 151,906 | 1,592,422 | 10.48 |
SH4 | 144,849 | 1,383,746 | 9.55 | SX19 | 143,270 | 1,344,168 | 9.38 |
SJ1 | 143,453 | 2,354,446 | 16.41 | SX20 | 144,038 | 1,352,983 | 9.39 |
SJ2 | 139,706 | 1,221,842 | 8.75 | SX21 | 144,141 | 1,298,644 | 9.01 |
SJ3 | 148,056 | 1,347,424 | 9.10 | SX22 | 145,000 | 1,224,795 | 8.45 |
SJ4 | 171,626 | 3,081,308 | 17.95 | SX23 | 142,066 | 1,189,055 | 8.37 |
SJ5 | 146,279 | 1,274,606 | 8.71 | SX24 | 150,371 | 1,563,158 | 10.40 |
SJ6 | 153,773 | 1,702,217 | 11.07 | SX25 | 153,599 | 1,678,791 | 10.93 |
SJ7 | 139,864 | 1,326,283 | 9.48 | SX26 | 148,364 | 1,362,955 | 9.19 |
SL1 | 150,344 | 1,497,548 | 9.96 | SX27 | 151,134 | 1,479,202 | 9.79 |
SL2 | 142,746 | 1,290,494 | 9.04 | SX28 | 152,221 | 1,635,532 | 10.74 |
SM1 | 144,398 | 1,334,945 | 9.24 | SX29 | 145,849 | 1,442,431 | 9.89 |
SM2 | 139,926 | 1,877,997 | 13.42 | SX31 | 146,580 | 1,511,018 | 10.31 |
SN1 | 142,636 | 1,782,163 | 12.49 | SX32 | 147,503 | 1,509,826 | 10.24 |
SN2 | 146,239 | 1,327,197 | 9.08 | SX33 | 148,484 | 1,394,929 | 9.39 |
SS1 | 134,045 | 1,351,964 | 10.09 | SX34 | 147,378 | 1,434,272 | 9.73 |
SX01 | 145,563 | 2,152,103 | 14.78 | SX35 | 146,085 | 1,356,216 | 9.28 |
SX02 | 136,493 | 1,474,738 | 10.80 | SX36 | 139,212 | 1,215,151 | 8.73 |
SX03 | 140,107 | 1,955,306 | 13.96 | SX37 | 141,906 | 1,452,165 | 10.23 |
SX04 | 137,242 | 1,734,153 | 12.64 | SX38 | 142,509 | 1,418,841 | 9.96 |
SX05 | 142,744 | 1,662,479 | 11.65 | SX39 | 144,886 | 1,457,086 | 10.06 |
SX06 | 141,570 | 1,858,567 | 13.13 | SX40 | 135,976 | 1,186,188 | 8.72 |
SX07 | 140,762 | 1,798,000 | 12.77 | SX41 | 106,088 | 1,140,162 | 10.75 |
SX08 | 142,846 | 2,119,727 | 14.84 | SX42 | 137,456 | 1,246,916 | 9.07 |
SX09 | 145,038 | 1,910,647 | 13.17 | SX43 | 141,769 | 1,457,711 | 10.28 |
SX10 | 147,941 | 1,680,924 | 11.36 | SX44 | 144,564 | 1,689,305 | 11.69 |
SX11 | 150,815 | 2,067,161 | 13.71 | SX45 | 144,316 | 1,591,007 | 11.02 |
SX12 | 137,667 | 1,510,621 | 10.97 | SX46 | 137,927 | 1,350,467 | 9.79 |
SX13 | 151,122 | 1,475,451 | 9.76 | SX47 | 146,675 | 1,493,755 | 10.18 |
SX14 | 139,948 | 1,141,327 | 8.16 | SX48 | 138,873 | 1,285,432 | 9.26 |
ID | SNP Number | Hetloci Ratio (%) | Integrity Ratio (%) | ID | SNP Number | Hetloci Ratio (%) | Integrity Ratio (%) |
---|---|---|---|---|---|---|---|
SB1 | 300,918 | 17.91 | 48.80 | SX15 | 340,669 | 19.00 | 55.25 |
SH1 | 279,620 | 17.93 | 45.35 | SX16 | 334,821 | 18.15 | 54.30 |
SH2 | 351,232 | 19.60 | 56.96 | SX17 | 266,597 | 16.87 | 43.24 |
SH3 | 343,657 | 19.14 | 55.74 | SX18 | 355,004 | 19.54 | 57.58 |
SH4 | 317,807 | 17.97 | 51.54 | SX19 | 327,964 | 18.31 | 53.19 |
SJ1 | 276,991 | 18.88 | 44.92 | SX20 | 322,766 | 17.95 | 52.35 |
SJ2 | 297,219 | 17.30 | 48.20 | SX21 | 323,363 | 17.86 | 52.44 |
SJ3 | 353,923 | 19.30 | 57.40 | SX22 | 345,938 | 18.78 | 56.11 |
SJ4 | 450,693 | 28.73 | 73.10 | SX23 | 336,435 | 18.48 | 54.56 |
SJ5 | 341,109 | 18.93 | 55.32 | SX24 | 346,155 | 19.22 | 56.14 |
SJ6 | 359,735 | 19.94 | 58.34 | SX25 | 364,002 | 20.11 | 59.04 |
SJ7 | 284,537 | 17.15 | 46.15 | SX26 | 343,732 | 19.22 | 55.75 |
SL1 | 349,578 | 19.69 | 56.70 | SX27 | 357,266 | 19.79 | 57.94 |
SL2 | 321,662 | 17.92 | 52.17 | SX28 | 354,589 | 19.76 | 57.51 |
SM1 | 321,841 | 17.88 | 52.20 | SX29 | 329,492 | 18.55 | 53.44 |
SM2 | 268,565 | 17.91 | 43.56 | SX31 | 310,206 | 18.43 | 50.31 |
SN1 | 295,616 | 18.08 | 47.94 | SX32 | 318,428 | 18.67 | 51.64 |
SN2 | 334,074 | 18.23 | 54.18 | SX33 | 337,137 | 18.91 | 54.68 |
SS1 | 274,926 | 16.70 | 44.59 | SX34 | 326,911 | 18.22 | 53.02 |
SX01 | 295,832 | 19.07 | 47.98 | SX35 | 332,924 | 18.43 | 53.99 |
SX02 | 267,309 | 17.33 | 43.35 | SX36 | 301,753 | 17.80 | 48.94 |
SX03 | 272,426 | 18.23 | 44.18 | SX37 | 287,012 | 17.57 | 46.55 |
SX04 | 267,987 | 17.77 | 43.46 | SX38 | 301,108 | 17.77 | 48.83 |
SX05 | 300,601 | 17.99 | 48.75 | SX39 | 315,850 | 18.54 | 51.23 |
SX06 | 279,522 | 18.32 | 45.33 | SX40 | 282,203 | 17.29 | 45.77 |
SX07 | 279,250 | 18.17 | 45.29 | SX41 | 302,783 | 8.39 | 49.11 |
SX08 | 279,198 | 18.55 | 45.28 | SX42 | 290,009 | 17.36 | 47.03 |
SX09 | 297,579 | 18.89 | 48.26 | SX43 | 287,487 | 17.25 | 46.62 |
SX10 | 323,345 | 19.13 | 52.44 | SX44 | 290,581 | 17.74 | 47.13 |
SX11 | 314,870 | 19.83 | 51.07 | SX45 | 300,420 | 18.20 | 48.72 |
SX12 | 271,604 | 17.61 | 44.05 | SX46 | 279,457 | 17.04 | 45.32 |
SX13 | 355,317 | 19.87 | 57.63 | SX47 | 315,801 | 18.34 | 51.22 |
SX14 | 317,163 | 17.48 | 51.44 | SX48 | 285,131 | 17.00 | 46.24 |
Population | HLJ | IM | JL | LN | HN | XJ |
---|---|---|---|---|---|---|
HLJ IM | 0.009 | |||||
JL | 0.007 | 0.005 | ||||
LN | 0.005 | 0.039 | 0.005 | |||
HN | 0.036 | 0.007 | 0.038 | 0.047 | ||
XJ | 0.001 | 0.012 | 0.005 | 0.003 | 0.020 |
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Li, J.; Wei, S.; Huang, Z.; Zhu, Y.; Li, L.; Zhang, Y.; Ma, Z.; Huang, H. Genetic Diversity and Population Structure in Solanum nigrum Based on Single-Nucleotide Polymorphism (SNP) Markers. Agronomy 2023, 13, 832. https://doi.org/10.3390/agronomy13030832
Li J, Wei S, Huang Z, Zhu Y, Li L, Zhang Y, Ma Z, Huang H. Genetic Diversity and Population Structure in Solanum nigrum Based on Single-Nucleotide Polymorphism (SNP) Markers. Agronomy. 2023; 13(3):832. https://doi.org/10.3390/agronomy13030832
Chicago/Turabian StyleLi, **hui, Shouhui Wei, Zhaofeng Huang, Yuyong Zhu, Longlong Li, Yixiao Zhang, Ziqing Ma, and Hongjuan Huang. 2023. "Genetic Diversity and Population Structure in Solanum nigrum Based on Single-Nucleotide Polymorphism (SNP) Markers" Agronomy 13, no. 3: 832. https://doi.org/10.3390/agronomy13030832