Development and Characterization of 177 SNP Markers in The Mud Shrimp Upogebia Major

doi:10.21203/rs.3.rs-724262/v1

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Research Article

Development and Characterization of 177 SNP Markers in The Mud Shrimp Upogebia Major

https://doi.org/10.21203/rs.3.rs-724262/v1

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published 20 Jan, 2022

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The mud shrimp Upogebia major (De Haan, 1841) (Crustacea, Decapoda, Gebiidea) is an important species widely distributed in coastal shallow waters. As an active initiation species, it has contributed significantly to the maintenance of coastal benthic biodiversity. However, there is still a lack of effective molecular markers to effectively protect and manage this species. In this study, we used the DNeasy Blood & Tissue kit to extract DNA and Illumina HiSeq 4000 sequencing technology to obtain SNP marker resources. 177 single nucleotide polymorphism (SNP) markers were developed and characterized in U. major. The minor allele frequency raged from 0.0500 to 0.5000. The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. Polymorphic information content ranged from 0.0905 to 0.3750. The inbreeding coefficient values varied from − 0.2902 to 0.5968. Seventeen loci showed significant deviations from the Hardy-Weinberg equilibrium (P < 0.05). The polymorphic SNPs will be helpful for the further population genetic analysis and natural resource conservation of U. major.

Conservation Biology

Molecular Genetics

Upogebia major

SNP markers

Population genetic diversity

Conservation genetics

The mud shrimp Upogebia major (De Haan, 1841) is one of the largest upogebiids, which forms massive populations in the upper sublittoral zone at depths of 0.5-3 m in slightly silted sand of the Japanese Islands, the Korean Peninsula, and the Shandong Peninsula (Selin, 2017). Like other hole-dwelling animals, it is an active edificator and defines the qualitative composition and abundance of the bottom fauna (Kinoshita et al., 2007) (Ubaldo et al., 2013). Besides the important role in the structure of benthic community,the phamaceutical value used by lactagogue was ecorded in Chinese Medicinal Animals. This arouses a strong interest in the study of this species. However, there are few studies on the population genetic investigation of U. major. At present, only a few studies have been conducted on the complete mitochondrial genome of U. major (Sun and He, 2021). In this study, we mainly studied the single nucleotide polymorphism (SNPs) of the mud shrimp U. major. SNPs are the most convenient and fast DNA marker in genetic studies because of their wide genomic distribution and high level of polymorphism (Liu et al., 2019) (Qu et al., 2019). Therefore, SNPs were developed and characterized in U. major with the restriction-site associated DNA tags sequencing (RAD-seq), and will provide important genetic markers for the studies of population genetic diversity and conservation genetics.

Muscle tissue was collected from 30 U. major individuals from Yantai in Shandong province (37°27′N/121°30′E). Genomic DNA was extracted using the DNeasy Blood & Tissue kit (QIAGEN, Germany) according to the manufacturer’s instructions. RAD library construction, sample indexing and pooling followed for the natural populations (Baird et al., 2008). To obtained SNP marker resources, pair-end (150-bp) sequencing was performed using Illumina HiSeq 4000 (Shanghai BIOZERON Co., Ltd), and a total of 719,728 putative SNPs in U. major was identified.

Using primer V3.0 to design primers, 175 primer pairs were successfully created. PCR reactions were performed in a 25 µl volume with GenStar PCR Mix according to the manufacturer’s instructions (GeneStar, Beijing, China). The PCR amplification procedure was as follows: an initial denaturation at 94°C for 5 min; then 40 cycles of 94°C for 30 s, annealing for 30 s (for annealing temperatures of each primer pair, see Table 1), and 72°C for 30 s; and a final extension at 72°C for 7 min. Amplified samples were purified by gel extraction and sequenced on ABI 3730 DNA Analyzer (Applied Biosystems). For validated loci, statistics including the minor allele frequency (MAF), observed heterozygosity (H_O), expected heterozygosity (H_E), polymorphism information content (PIC), inbreeding coefficient (F_IS) and P value representing the deviations from Hardy-Weinberg equilibrium (HWEP) were caltulated using Cervus 3.0 (Kalinowski et al., 2010).

One hundred and seventy-five primer pairs could be amplified, and 177 SNPs located within these sequences were confirmed by Sanger sequencing. The minor allele frequency raged from 0.0500 to 0.5000 (Table 1). The observed heterozygosity and expected heterozygosity ranged from 0.0333 to 0.9000 and from 0.0966 to 0.5085, respectively. Polymorphic information content ranged from 0.0905 to 0.3750. The F_IS values varied from − 0.2902 to 0.5968. Seventeen loci showed significant deviations from the HWE after Bonferroni correction (P < 0.05). These polymorphic SNP markers will be useful for further population genetic analysis, natural resource conservation and selective breeding of U. major.

Acknowledgments: This work was supported by National Natural Science Foundation of China (31460562); Shandong Provincial Natural Science Foundation, China (ZR2020MD002); the Doctoral Science Research Foundation of Yantai University (SM15B01, SM19B70, SM19B28).

Conflicts of interest/Competing interests: The authors have no conflicts of interest to declare that are relevant to the content of this article.

Availability of data and material: All data analysed during this study are included in this published article.

Code availability: Not applicable.

Ethics approval: Not applicable.

Consent to participate: Not applicable.

Consent for publication: Not applicable.

Author contributions: Corresponding author contributed to the study conception and design. Ying Qu, Yan Ni and Zilin Jiang helped collect samples. Donghui Sun and Jirui Zhang were in charge of extracting genomic DNA. Shukui Zhang, Zhikai Xing and Sen Wu helped collect the data. Chenghong Wang and Yunqi Song were in charge of compiling the data. The first draft of the manuscript was written by Chenghong Wang and all authors commented on previous versions of the manuscript. Corresponding author read and approved the final manuscript.

Baird NA et al (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. Plos One 3(10):e3376. https://doi.org/10.1371/journal.pone.0003376
Liu KK, Yu H, Li Q (2019) Development and characterization of 108 SNP markers in the Iwagaki oyster, Crassostrea nippona. Conserv Genet Resour 11(4):437–442. https://doi.org/10.1007/s12686-018-1047-7
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment (vol 16, pg 1099, 2007). Mol Ecol, 19(7): 1512–1512. https://doi.org/10.1111/j.1365-294X.2007.03089.x
Kinoshita K, Wada M, Kogure K, Furota T (2007) Microbial activity and accumulation of organic matter in the burrow of the mud shrimp, Upogebia major (Crustacea: Thalassinidea). Mar Biol 153(3):277–283. https://doi.org/10.1007/s00227-007-0802-1
Qu J, Wang S, Cui Y, Guo X, Wang Y (2019) Development and characterization of 26 SNP markers in Nipponacmea schrenckii. Conserv Genet Resour 12(2):195–198. https://doi.org/10.1007/s12686-019-01095-x
Selin NI (2017) The population dynamics and growth of the mud shrimp Upogebia major (De Haan, 1841) (Crustacea: Decapoda) from Peter the Great Bay, Sea of Japan. Russ J Mar Biol 43(4):270–275. https://doi.org/10.1134/S1063074017040101
Sun X, He J (2021) The complete mitochondrial genome and phylogenetic analysis of Upogebia major (De Haan, 1841). Mitochondrial DNA B 6(3):970–971. https://doi.org/10.1080/23802359.2020.1870898
Ubaldo JP, Nanri T, Takada Y, Saigusa M (2014) Prevalence and patterns of infection by the epicaridean parasite, Gyge ovalis and the emergence of intersex in the estuarine mud shrimp, Upogebia major. J Mar Biol Assoc UK 94(3):557–566. https://doi.org/10.1017/S0025315413001392

Table 1

Development and characterization of 177 SNP markers in the mud shrimp *Upogebia major*
Primer ID	Primer sequence (5′–3′)	Size(bp)	T_m(℃)	SNP type	SNP position	H_O	H_E	F_IS	HWEP	PIC	MAF
2342_2	F: AGTCAGGCTGAAGTGATGAAACT R༚CGATGCTGCACAGAGATCCT	309	60	A/C	73	0.4000	0.3254	-0.1097	NS	0.2688	0.2000
5675_2	F: ACAGGGAGACAAGCGGTTTC R༚CGTGGCGAATGAAAGTAGCG	259	60	T/C	95	0.8667	0.4994	-0.2765	*	0.3705	0.4333
6217_1	F: ACATTTGTCGTCAGCTGGTG R༚TGCCTTCATTACTTTGCCCA	294	59	C/A	91	0.8667	0.4994	-0.2765	*	0.3705	0.4333
7952_1	F: TTTCACAGATAAGCCTGGCT R༚GCCAGCAATTTCCGCATCAT	338	60	G/T	68	0.7333	0.4723	-0.2244	NS	0.3566	0.3667
8984_2	F: GACTGTGTCCTGCTGATGTT R༚CTGGGGATGTTCAGCCATGT	256	60	A/G	84	0.5000	0.3814	-0.1423	NS	0.3047	0.2500
9719_1	F: ACAGATGTCGATTCGCAGTGA R༚AGCATAGTCGCTTTAGCCCC	282	60	A/G	67	0.8667	0.4994	-0.2765	*	0.3705	0.4333
9719_2	F: ACAGATGTCGATTCGCAGTGA R༚TGTTCACCCCACGAGCATAG	265	60	T/G	84	0.8667	0.4994	-0.2765	*	0.3705	0.4333
10117_2	F: ACGTGTTGTGTCGTCTGTGT R༚AGTAGCAGACAGGAGGAGGG	292	60	T/A	71	0.3000	0.2593	-0.0778	NS	0.2225	0.1500
14865_1	F: TTTAATAGTATTGTGTAGAGGGAGG R༚CGACGAGTATAGCGACCACC	277	60	G/A	56	0.2000	0.2825	0.1628	NS	0.2392	0.1667
18507_1	F: ACAGATGTCGATTCGCAGAGA R༚ACGGGCTCTAAATGAGTGGA	319	59	G/T	109	0.7000	0.4627	-0.2120	NS	0.3515	0.3500
20936_1	F: ACGGATCAGTCAAGTCGTGT R༚TTTGTGCCATCATGGGTGGA	312	60	G/A	64	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
26102_1	F: CGGCTGCCGTATCAATAGC R༚ACGCCTTGCTACGTAGTACC	305	60	C/A	104	0.8000	0.4881	-0.2499	NS	0.3648	0.4000
28472_1	F: ACTCAATAGACTACCCTCTCAAGG R༚ACTTCCTTGTCGTGAAGCGT	316	60	C/T	63	0.9000	0.5034	-0.2902	**	0.3725	0.4500
35998_1	F: ACAAATGTCGATTCGCAGTGA R༚TCGCGCAACCAACAGAAAAG	307	60	C/A	88	0.9000	0.5034	-0.2902	**	0.3725	0.4500
37685_2	F: AGGTAAAGCGCAGACAAACG R༚TTCCTCACATCAAGAGCCAA	245	59	C/A	78	0.6333	0.4401	-0.1879	NS	0.3391	0.3167
43946_1	F: GTCTGTCAGACCCACGGTG R༚AGCCTGTAAAGTCAGTGACAGA	282	60	C/A	40	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
63249_1	F: TGTGCCCAATATAACAGTGCAG R༚GGAGGCTGTGTAACGTGGG	282	60	A/C	71	0.9000	0.5034	-0.2902	**	0.3725	0.4500
96754_1	F: TCCATCTGTGGTTGTGTAGCT R༚GTTTCCTCGCGCTATGCATG	356	60	C/G	72	0.9000	0.5034	-0.2902	**	0.3725	0.4500
109215_1	F: ACAGATGTCGATTCGCAGTGA R༚GGACCCAACCCGGTATGAAA	283	60	G/A	82	0.8667	0.5062	-0.2703	*	0.3739	0.4667
109744_1	F: AATTCTGTGGTATTCAGCTGT R༚TCAACCACCCTTGGATGAGC	273	60	C/A	71	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
112887_2	F: AGAACACTAACCTCAACAATTGGT R༚TCCAAGCTTCCATTCGTGGG	333	60	A/G	87	0.9000	0.5034	-0.2902	**	0.3725	0.4500
124474_2	F: TCTTTTGCGTTATTTCACATTGT R༚ATCATGCCTTAGCTTGCACT	293	58	C/T	47	0.8667	0.4994	-0.2765	*	0.3705	0.4333
126155_1	F: GGACAGCAGTCTCTTTAGTACT R༚TGCTTGTCTGTCAGTAGCCTG	287	60	A/G	100	0.0667	0.1266	0.2931	NS	0.1167	0.0667
133592_1	F: GCAATGAAACGCACCCAGAA R༚CCAGGAATGCGGTGGTTTTC	244	60	A/C	49	0.0667	0.1831	0.4489	NS	0.1638	0.1000
134738_1	F: TGAACATATGTCGATTCGCAGTG R༚TAACCCTTTCCAACCTGGCG	283	60	A/G	86	0.1000	0.2096	0.3445	NS	0.1849	0.1167
135002_1	F: ACTGTACAAGCTAAGAAAAACACCG R༚TCTGATGTACTTTTGTGTGCTGT	330	60	G/A	65	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
135764_1	F: ACGCAAAGGTTGGCCAAATC R༚TTGCGCACTGTTTTGTCGAG	313	60	C/T	67	0.8000	0.4881	-0.2499	NS	0.3648	0.4000
135891_1	F: TTCAAATGAGCTACAGGTGAGA R༚GCCATGAATAGTCCCGCCAT	294	60	C/T	88	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
135903_1	F: ATGACGAGACACAAACCCCC R༚GGTGCTAGGTAGTGGATTGGG	331	60	T/C	106	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
136266_1	F: TTACCTGATTCATTTTAAAGAATGGT R༚TGGAAACAGCCTGGCAATTC	295	59	A/T	81	0.8667	0.5062	-0.2703	*	0.3739	0.4667
136602_1	F: ATTCTGCTGGCTCGGGTAAC R༚ATCCCGCTATTTGCCCAACA	332	60	T/A	69	0.1000	0.1554	0.2076	NS	0.1411	O.O833
137241_1	F: CCCATGAAAGAGGGCGAACT R༚TGTCCTCACTGCTCTGACCT	340	60	A/T	43	0.1667	0.2096	0.1058	NS	0.1849	0.1167
137471_1	F: TTCCTCACTTCTGGGTCCGA R༚TTGGTAATTGCACGTGTTGT	316	60	G/A	106	0.1000	0.1554	0.2076	NS	0.1411	0.0833
137488_1	F: CGTTGTTTTCATTCCGCTTTCG R༚CTCCTTCTCTGCCTCCTCCT	352	60	T/C	50	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
137562_1	F: TGTCGATTGGCAGTGAAAAACT R༚GTTGCTCCTCCTCCACCATC	316	60	T/C	107	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
137566_1	F: TTCTCTGGCTTTGATGGTTT R༚CTCTCGTATCCGACTGCACC	342	60	G/A	90	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
137731_1	F: TCGAATCCTACCTGTCCAGA R༚GCTCATCAGGTAGGCCAAGG	340	60	T/C	61	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
137790_1	F: TGACTGAGATGACCCAACTCA R༚CACGAAGGGGCGTCATTTTC	274	60	T/C	86	0.1000	0.1554	0.2076	NS	0.1411	0.0833
137803_1	F: GTGTCTGTGCTAGTGGGAGG R༚CACACACACACACACACACA	274	60	T/A	99	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
137820_1	F: AATCACATCTGGCCTCTGAT R༚ACGGCTCTGCATAACAAACG	303	59	T/G	89	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
138017_1	F: ACCTTCACAATTTACGTTAATCGACA R༚CCCGTATCAGTAACCCTGGC	326	60	A/T	92	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
138166_1	F: ACGGAAGTGTATCGTTGTTGT R༚AGGTGAGGGATGAAGACTTGG	260	59	A/C	59	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
138172_1	F: TGAACAGATGTCGATTCACAGTG R༚CAAAAATTCCCTCAGCCCGC	343	60	T/A	66	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
138186_1	F: TGAACAGATGTAGATTCGCAGTGA R༚GCAAGGTCTGTGTGTCCTGA	328	60	A/T	54	0.9000	0.5034	-0.2902	**	0.3725	0.4500
138329_1	F: TTGTGCCCTCTGGTTCACTC R༚GCTGCAAGCAGTAAAACACCA	281	60	T/C	43	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
138496_2	F: GGTGGCGTAAGTACTTCAAGC R༚TGGGTAATGTTCACCTCGGC	310	60	C/A	81	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
138539_1	F: TGAACATATGTCGATTTGCAGTGA R༚CCTGTACCCAATTTTGCGCC	336	60	G/A	98	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
138849_1	F: CCCGCTGCTTTTCCCTTTTT R༚ACACTTCGTTGTCAGCCTGT	273	60	T/C	94	0.1333	0.1831	0.1488	NS	0.1638	0.1000
139132_2	F: CATGAGCGAACAATGCCTCG R༚TGACTGGCAACCTCTCGTTC	326	60	A/G	79	0.3333	0.2825	-0.0884	NS	0.2392	0.1667
139146_1	F: TGACAAGTTGGAAATTTTGTCGAGT R༚AGCATGAGACAGATTGCGGG	335	60	A/G	60	0.2333	0.2096	-0.0567	NS	0.1849	0.1167
139166_1	F: TCGCAATTTGCTTATGTATCGGA R༚TGGTGGTAAGTAGTCTTCATAATCAGG	254	60	A/C	83	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
139234_1	F: TCTCCAATTTTATGTTTTTACTCGCT R༚CCACTGAACCAAGGGACGAT	321	60	T/C	102	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
139453_1	F: GCTTGGTTTTACGTTGCAAATGG R༚AGTCTATGGTGGATCACTCTGC	333	60	T/C	86	0.1667	0.2096	0.1058	NS	0.1849	0.1167
139485_1	F: TCGTAGCAAGATTTATAATACGGTGA R༚TCTCTGAGGGCTGTAAGGCT	333	60	G/A	77	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
139529_1	F: TGGCTTATGCAGAAAGGCCA R༚TGCACTGCATCGTTTCTTGC	320	60	T/G	105	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
139593_1	F: TGGATTGAAATTTTTCATTATCGAGG R༚CTGCGTCAAGTGGGGGTTAT	294	60	G/T	69	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
139796_1	F: ACAGATGTCGATTCGCAGTGA R༚ATGCATACAGACAGACAAACA	270	60	G/C	98	0.2000	0.2825	0.1628	NS	0.2392	0.1667
139863_1	F: TCAACGCAAAGATGGTCACA R༚AACGGTGCCACCTATGAAAA	313	58	G/T	37	0.2000	0.2350	0.0722	NS	0.2044	0.1333
139883_1	F: AACCACGCAGGCACCTTTAT R༚TTTCTGCTTCCCCTCCTCCT	256	60	A/G	92	0.2000	0.2350	0.0722	NS	0.2044	0.1333
139892_1	F: TGTTAGCGAATTTGGGGCCT R༚GCAGTTCGGAAGAGAGGGAG	299	60	G/C	99	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
139977_1	F: GACAGGCAGGAAGGAAGGAC R༚CCCGAACCTTTTCTGCCTCT	288	60	T/C	66	0.2667	0.3254	0.0909	NS	0.2688	0.2000
140068_1	F: ACAGGCATTTCCCACTATCCA R༚ACCACTGCTCTACGTAGACCA	329	60	T/C	55	0.2667	0.3254	0.0909	NS	0.2688	0.2000
140071_1	F: TCTTCCTTCTCTTCTTCCTTCA R༚CTCCTAATTCCGCCTCCACC	329	60	C/T	29	0.4667	0.5062	0.0323	NS	0.3739	0.4667
140071_2	F: TCTTCCTTCTCTTCTTCCTTCA R༚CTCCTAATTCCGCCTCCACC	329	60	G/A	64	0.4667	0.5062	0.0323	NS	0.3739	0.4667
140180_1	F: TTCGTGATACAGTCTTCTGAAA R༚ACCAACAGTCTTTGCAACGC	308	60	C/T	77	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
140308_1	F: TCCTATGTATTCCCTGCATGTCG R༚TGCTCCCATCCACAGTGAAC	337	60	C/T	92	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
140586_2	F: CTCTCTAAGCGGCGTTAGGG R༚CGGAAAGAGTGTTGGTGGGA	314	60	C/T	65	0.2333	0.2593	0.0444	NS	0.2225	0.1500
140778_1	F: TTCTTCCTGTTTTGACGCGC R༚GTGACTGTTAGTGAGTTGCCG	337	60	G/A	99	0.2333	0.3045	0.1241	NS	0.2546	0.1833
140821_1	F: AAATTCAAAGTAGAATAACATGGTCT R༚TCGATCACTTCCTCCAGGGT	319	60	G/A	89	0.3000	0.4130	0.1503	NS	0.3236	0.2833
140914_1	F: GAGGAGCAGCAGATTCCCAC R༚GGGACGTTTTGACAGTGGGA	334	60	G/T	79	0.7333	0.4723	-0.2244	NS	0.3566	0.3667
140956_1	F: ATTCGCCACAACAAACGGTG R༚TGTCCCATGGCTGATTGTCC	306	60	G/A	33	0.2667	0.3638	0.1459	NS	0.2938	0.2333
140959_1	F: AGGGAGAGAATAAGTCTGTCA R༚CGTTACAAGGAGAGTCCGCA	343	60	A/G	62	0.4000	0.4271	0.0244	NS	0.3318	0.3000
140963_1	F: ACAGATGTCGATTCGCAGTGA R༚TCTACTCCACAAAGCCTCCC	321	60	G/A	67	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
140990_1	F: AACAGTTTCGGCAGCTTCCT R༚CATCTGTGTCAGGGCTCGAG	343	60	G/A	52	0.4000	0.3254	-0.1097	NS	0.2688	0.2000
141091_1	F: CTGTGAACAGCAGTCGACCT R༚AACTGGATGGTGACTGCTGG	333	60	G/A	95	0.2667	0.3977	0.1892	NS	0.3146	0.2667
141156_1	F: ACCCAAGACTGAAGACCGAAC R༚TGTTCGTCCTTTTGGGGTGT	260	60	C/T	78	0.5333	0.3977	-0.1534	NS	0.3146	0.2667
141181_1	F: GAGGAAAAGAGCTGCAGTAGGA R༚TCATAGCTCCACTGCCATGG	259	60	A/C	80	0.3667	0.4130	0.0510	NS	0.3236	0.2833
141183_1	F: TCACACTTTCTTCCTCTTTTTCA R༚ACCCAACCCCATCTTGTTTGT	330	60	C/T	56	0.3000	0.2593	-0.0778	NS	0.2225	0.1500
141487_1	F: TCCGAAAGTCATTAAATTTCCATGA R༚TCATCTCGACGTGAGCTTCG	346	60	G/A	105	0.4000	0.3254	-0.1097	NS	0.2688	0.2000
141545_1	F: TCGGTATTTCGAAGCGAACT R༚AATCGACCGGAAACTGGTCT	297	59	C/T	32	0.4000	0.3977	-0.0112	NS	0.3146	0.2667
141565_1	F: TCCTGTATTCCTTGCGTGTCA R༚ATGGAACTAAAATACTAAGATTGCAT	338	59	A/G	90	0.4000	0.4881	0.0909	NS	0.3648	0.4000
141652_1	F: TCGAGCGTTGCACAATATTGA R༚GGGTAAACTGTGGAAGGGCT	338	60	G/C	108	0.3667	0.4627	0.1075	NS	0.3515	0.3500
141762_2	F: TTCGCAGTGGAAAAAGGTGT R༚GGACAGTGCGGTGACTTTGA	288	61	A/G	80	0.9000	0.5079	-0.2862	*	0.3747	0.4833
141795_1	F: ACAGATGTCGATTCGCAGTGA R༚CACCCGCCATTCAATGCTTC	337	60	T/G	93	0.9000	0.5034	-0.2902	**	0.3725	0.4500
141832_1	F: GTTCTCTTGGGAGCGAGACG R༚CCTTCTCGCCTCCTCTCAAC	317	60	C/T	72	0.6000	0.4271	-0.1762	NS	0.3318	0.3000
141972_2	F: CAAGGACATACACGGGCACT R༚TACTTGCCCTCGTTCCAGTG	332	60	G/A	106	0.7000	0.4627	-0.2120	NS	0.3515	0.3500
141991_1	F: AACAGACGTCGATTCGCAGT R༚GGGTCACCAAAAACGTGAAGG	281	60	A/C	43	0.5000	0.4944	-0.0141	NS	0.3680	0.4167
142068_1	F: GTTGAAACGGAGGATGTAATTTCGA R༚CCAACGATGAAGTGAGCAGC	340	60	C/T	69	0.5667	0.4627	-0.1093	NS	0.3515	0.3500
142089_1	F: TTTTCCTAACTAGTAAAACGCCT R༚CGCATGGAAGCAAAGCTCTC	277	60	G/C	54	0.7667	0.4944	-0.2239	NS	0.3680	0.4167
142234_1	F: ACAGATGTCGATTCGCAGTGA R༚CACCACAAAACCGAGGATGG	293	60	C/T	108	0.8667	0.5085	-0.2683	*	0.3750	0.5000
142735_1	F: TGTGGGATCCATGATGCAGG R༚CCCACCTGTTTGTTCCCACT	339	60	C/T	80	0.0667	0.1266	0.2931	NS	0.1167	0.0667
151278_1	F: TCAAAGGGTAAAAGTGTCATGT R༚GGTCCTTGCAAGGCTGTTTG	284	60	T/C	91	0.4000	0.3254	-0.1097	NS	0.2688	0.2000
159979_2	F: TCAGCTGGTCCGTTGGTTTT R༚ATGGTGCCACAAAACAGTGT	296	60	C/T	69	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
196855_1	F: TCATTTGGTGTTGGATACTGATCT R༚GGACACCATTTCCAAAGTGAGTG	344	60	C/T	71	0.7667	0.4808	-0.2370	NS	0.3610	0.3833
196932_2	F: CGGTGTCCTTCTCTGAGTGG R༚TTTGGAGCAACACCCCGATT	287	60	C/T	45	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
197553_1	F: TGCGACTTTACATGTGCGTC R༚GGACACTGTACGCTACCGG	265	60	C/T	63	0.1333	0.2825	0.3510	NS	0.2392	0.1667
201056_2	F: GTACCCAGGTGCCCAGTTC R༚ACACCACACCACACAACACT	321	60	A/T	72	0.0333	0.1554	0.5968	NS	0.1411	0.0833
205020_2	F: ATGCAGACATGGGCGAGAAA R༚AGGAAGTATCAACAGCAACTCCA	286	60	C/T	53	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
205068_2	F: TCAGTGGTTGATTGTAGCCAGT R༚GGCTACGAGTCGATGTCAGT	286	60	C/T	52	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
205190_2	F: GTGCGTCAAAATCCTGCCAA R༚CTCTCAGTCAGCCCCGTAGA	280	60	C/T	47	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
205281_2	F: GTAAGCTGGGGAGGTGTACG R༚CTCTCCTCCCTCCTCTTGCT	329	60	C/A	84	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
205522_2	F: ATTCACAGCGACCTTCCTGG R༚CACTGCCACAGTTGTGTTGG	317	60	A/G	82	0.1333	0.1831	0.1488	NS	0.1638	0.1000
205570_2	F: TGTTCAGCGATTCGTCTGCA R༚TCCTGGAACACACAATTTTTGCA	257	60	C/T	64	0.1000	0.1554	0.2076	NS	0.1411	0.0833
205723_2	F: GTACAAAGCCTCAACACACCG R༚CCCACCATCTACACCAGTGG	289	60	A/G	81	0.0667	0.1266	0.2931	NS	0.1167	0.0667
206029_1	F: AATGACCCGACTCAACGTCT R༚CCTCACCTTGCAACACTGGT	330	60	C/T	51	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
206073_2	F: TCCATCGTCCAGGTAGACTGT R༚CCGCCAATAACTGCAAAGGG	352	60	G/A	78	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
206126_2	F: ACATGGTTCAGAAAGTTGAAGA R༚CAACTGTGCCACAAATGCGA	305	60	A/T	99	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
206423_2	F: AGCCACACACGATAAGACCC R༚GCCCTTACTCACACTCCCAC	332	60	C/A	42	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
206630_1	F: TGTTATAAAGTACTTTCTGCAGAGT R༚GAGTATGTAACGCCCGCTCA	315	60	C/T	45	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
206677_2	F: TGAACAGATGTCGATTCACAGTG R༚TGCAGCAATTTATAAACACCATTCA	341	59	G/A	90	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
207162_1	F: TCCCTGCGTGTTATAAGAGCT R༚TCCCTCAACTAGGTATGATTTCCT	259	59	G/A	59	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
207365_2	F: AGATGCTCATTTGGCTTGGC R༚AGCTGTTGGACGGTAGGATT	264	59	T/C	85	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
207425_2	F: TCACGGGAAATACATTGAGCA R༚GTCTGTGCTTGCAACTCGTC	256	60	C/G	102	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
207490_2	F: TATCATGGTGCTTGGGTGGC R༚TCTGCATCAAGTGTGTGCCA	267	60	A/G	110	0.1000	0.1554	0.2076	NS	0.1411	0.0833
207539_2	F: GCTTCCTCCAGAGTCGCATC R༚TCCGTCGCCAATCAGATAGC	291	61	A/G	94	0.1000	0.1554	0.2076	NS	0.1411	0.0833
207554_1	F: GGAACGTGCAGATTTCCAGC R༚GTGGTGCCACATCTCTTCCA	291	60	A/G	57	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
207650_1	F: TCCCACATATCCACTGCGTG R༚GGCAAGCAACTGTCCCCATA	318	60	T/C	84	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
207684_1	F: TCTTCACAATTTTACCTTCGCA R༚AAAGCTGTGACAAATGGCCG	349	60	C/T	49	0.1000	0.1554	0.2076	NS	0.1411	0.0833
207728_2	F: TCATCGTGCAGTTCTTACAGT R༚AAACGCCTATGTTCGTGGGT	317	60	C/A	52	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
207730_1	F: ACAGATGTCAATTCGCAGTGA R༚ACAAACGGCGGAAATGTGTG	334	60	C/A	63	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
208318_2	F: AGGGCTAGAGTTATAGAGGGCT R༚GAATGAAGGAGAGGCTGGGC	316	60	C/T	47	0.1000	0.1554	0.2076	NS	0.1411	0.0833
208453_2	F: ATTCATTACATGCGGGGGCA R༚TTGAATGTCAACTTCGCCGC	289	60	C/A	54	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
208568_2	F: ATTCTGCCTCTGTCACACCG R༚TCCATTATCATCACTTGTCAGCT	276	60	C/G	66	0.2333	0.2096	-0.0567	NS	0.1849	0.1167
208577_1	F: ACTATTCATAGCCATAAACCACA R༚CCACAAATCAGTGTATGGTGGC	321	60	C/T	44	0.1333	0.1831	0.1488	NS	0.1638	0.1000
208717_2	F: ACTGATGAAGACGGGTATCGC R༚CACTGAATGTTGTGGGTCGC	303	60	C/A	82	0.1333	0.1831	0.1488	NS	0.1638	0.1000
208822_2	F: ACGTAGACAGACACACAACGA R༚CCCTCCAACTTTCCCCATCG	278	60	T/G	52	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
208828_2	F: AATTCATCGAGGCGCTGGAT R༚TGGCCGATTCCACATACGTT	340	60	C/T	108	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
209004_2	F: TGAACAGATGTCGATTGGTAGTGA R༚TCTGCTTACACCAGCTTGCA	291	60	A/C	102	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
209120_2	F: ACACTACACTGACAGAGGTGTG R༚TGTCAAACCTATGCACCGCT	328	60	A/G	82	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
209159_2	F: AGATGTCGATTCGCAGTGAA R༚CGCAGAGGACAGACGAACTC	268	60	T/C	56	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
209249_1	F: ATGTCAGGTTTTCTCTCCCT R༚CGAATCCTCATAGGCCTGCC	325	60	G/A	89	0.1667	0.2096	0.1058	NS	0.1849	0.1167
209286_2	F: ACACTCTTTTGAAATGTTGTGCA R༚CCCCGGGTCTCCTTCTTCTA	335	60	C/T	62	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
210043_2	F: ACACCTTTCGAGTCTTCACCA R༚TGCCTCCTCATAAACACTGTGT	306	60	T/A	72	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
210089_2	F: GCCACTTTCATTTCAGCCCC R༚TTGCAGCAAAAGCTCACACA	326	60	C/T	65	0.1667	0.2096	0.1058	NS	0.1849	0.1167
210100_2	F: TCACAACTGCACTGTAATGTGT R༚AGGAGATGGACCAGGAGAGA	329	59	A/G	92	0.2333	0.2593	0.0444	NS	0.2225	0.1500
210197_1	F: TTCAAGATTTTGTAAGCAATTTAGAAT R༚ACATGTGGAACTGAAAAGCGG	349	59	C/A	97	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
210217_2	F: GTGTTAGCGAATTTGGGCCC R༚ACAGATGTCGATTCGCAGTGA	341	60	T/A	78	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
210222_1	F: ACCCCAAAGAGCAAAAACCA R༚GCCACAAGCAACAGTGGTTT	336	60	A/G	97	0.1333	0.1831	0.1488	NS	0.1638	0.1000
210380_1	F: TGGTCACTCTAGGTCTGCCA R༚TGGCAATGTGAATACCGTGT	274	60	A/G	99	0.1667	0.2593	0.2094	NS	0.2225	0.1500
210447_1	F: ACCTTGCGTTCCATACCGAG R༚CTGTCTGGCTGGACTGTCTG	335	60	C/T	71	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
210590_2	F: ACTTTAACCCTTTCACGCCTGA R༚AGCAGGCGTTTGACTTCTGG	247	61	G/C	105	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
210908_1	F: AACGCAAATAACATAGTTAAGCACA R༚ACAACAGAATACCCGAGTCAGT	266	59	G/A	64	0.1667	0.4130	0.4180	NS	0.3236	0.2833
210949_2	F: TCCACATAAAGAAAATCGACGT R༚AAGTCTGGGTGTCTCGGTCA	334	60	G/A	55	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
210957_2	F: ACCACTGATGTGTAGGGTGT R༚GAGCGGGTGTATATTCGCCT	348	60	C/T	47	0.1667	0.1554	-0.0358	NS	0.1411	0.0833
211154_1	F: ACAGATGTCGATTGGCAGTGA R༚ACACCTGCTGATCCTTGCAA	304	60	G/T	49	0.2000	0.2825	0.1628	NS	0.2392	0.1667
211179_2	F: ATTGGGGGTTGCAGTTCTTT R༚AGCAAAATTGTTCTTTGATGCCA	292	58	G/A	73	0.1667	0.2593	0.2094	NS	0.2225	0.1500
211219_2	F: TGAACAGATATCGATTCGCAGTG R༚GGAAGACGGACAATGGAGCA	281	60	T/C	59	0.2333	0.3045	0.1241	NS	0.2546	0.1833
211287_2	F: TGCCAGAAAACAATTCCTGCA R༚AAGAGCTGTGTTCGGTCTGT	283	59	T/C	103	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
211328_2	F: ATGAACCACGCAGACACCTT R༚AAACCATACGTCCTGCAGGG	315	60	C/G	62	0.1333	0.1266	-0.0258	NS	0.1167	0.0667
212467_2	F: TCGTCAACTGACTGATAATGCT R༚TCGAACTCCCTCCAGACAGA	337	60	A/G	97	0.3667	0.5079	0.1533	NS	0.3747	0.4833
212480_1	F: AGAGCCAGAACTAACAATAAGCA R༚TTCCCCGTTATCCAACCACC	324	60	A/T	71	0.2667	0.2350	-0.0672	NS	0.2044	0.1333
212580_2	F: ACGAGAAAAACAACAGAACTGGG R༚GGGTGAAGGTCAACAATGAGG	347	60	G/C	82	0.2333	0.2593	0.0444	NS	0.2225	0.1500
212695_1	F: ACAGATGTCGATTCGCAGTGA R༚AGCTAGCCATGACTTCCTCA	281	60	A/T	55	0.2333	0.3045	0.1241	NS	0.2546	0.1833
212715_1	F: AGGAAACAAGTCAATGCCAAGT R༚TGTGATTCAACAAGTTTACCGTGT	271	59	C/T	58	0.2333	0.3045	0.1241	NS	0.2546	0.1833
212784_1	F: ACAGATGTCGAATCGCAGTGA R༚ACAACTCGGGTCACCAACAG	343	60	A/G	34	0.3667	0.3045	-0.0990	NS	0.2546	0.1833
213359_1	F: TCCCTTGCCCAACTGTCCTA R༚TTACCGTATGTGGGGCTGTG	279	60	G/A	44	0.3667	0.3814	0.0112	NS	0.3047	0.2500
213359_2	F: TCCCTTGCCCAACTGTCCTA R༚ACAGGTGCTTGTCAGGTACC	312	60	A/G	79	0.4000	0.4994	0.1022	NS	0.3705	0.4333
213445_1	F: TCACCCAGACAATTTCTAACAGTCA R༚GCGATCCAGTAGTCCTCAGC	316	60	A/C	28	0.3667	0.4401	0.0827	NS	0.3391	0.3167
213445_2	F: TCACCCAGACAATTTCTAACAGTCA R༚GCGATCCAGTAGTCCTCAGC	316	60	A/T	91	0.3333	0.3638	0.0354	NS	0.2938	0.2333
213458_2	F: ACAGATGTCGATTCGCAGTGA R༚TCTCATTTGTTGTGCTGCGC	301	60	C/G	88	0.3667	0.4401	0.0827	NS	0.3391	0.3167
213469_1	F: CGGTGATGTTCAGAAATTGGCA R༚ACATCATAACTGAGGCGCCC	317	60	A/G	73	0.9000	0.5034	-0.2902	**	0.3725	0.4500
213475_2	F: ACGACTCCATTCTGTTCACCT R༚CTCAGGAGTGAAAACAATCCGG	310	59	T/G	99	0.3000	0.2593	-0.0778	NS	0.2225	0.1500
213600_1	F: ACAGATGTCGATTCGCAGTGA R༚AGGTCTCATTGCGTGTGAAAG	268	60	A/T	97	0.5333	0.3977	-0.1534	NS	0.3146	0.2667
214019_1	F: TAAGAGTTGCGCCATGTCCA R༚AGATCACGTCAAGGGGAACA	259	60	G/A	57	0.4000	0.3254	-0.1097	NS	0.2688	0.2000
214038_2	F: TAACCCTTTCCAACCTGGCG R༚ACCTGTAACAAAATCCAGAGTT	301	60	T/G	91	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
214045_1	F: ACAAAGACTTTCATGTTAGAGGT R༚TCGTCTTCTCAAATGGGGGC	270	60	T/C	43	0.2000	0.2350	0.0722	NS	0.2044	0.1333
214045_2	F: ACAAAGACTTTCATGTTAGAGGT R༚TCTCAAATGGGGGCCGTAAC	302	60	C/T	52	0.4667	0.4881	0.0141	NS	0.3648	0.4000
214185_1	F: TCGTCTTGGGAGGAATTGGG R༚GCAGTCTTCTTTCGCCTCCT	303	60	A/G	90	0.4333	0.5079	0.0709	NS	0.3747	0.4833
214226_2	F: CACCGTAGTGTACAGCCTGC R༚ACTAACTGCCCAACCTCTGC	315	61	C/G	72	0.7333	0.4881	-0.2088	NS	0.3648	0.4000
214260_2	F: AAGTCCGCTACTGAACCCCT R༚TCGTGTCCAAGGGAGAAGGA	319	61	A/G	76	0.2000	0.1831	-0.0462	NS	0.1638	0.1000
214302_2	F: TCAACAACTTTCACTACATCTGT R༚GGCTAGACGTGAAGGTGACC	280	60	A/T	86	0.4667	0.4994	0.0255	NS	0.3705	0.4333
214321_1	F: CCAGGAGAGTGAAAGGCGTA R༚CTTGGGCAACAACCTCACCT	298	60	A/G	45	0.5000	0.4808	-0.0280	NS	0.3610	0.3833
214327_2	F: TGAGTTTGTGGTTTGCGGTG R༚ATCATGCTGAGAGGCAGTGG	328	60	T/C	57	0.7667	0.5079	-0.2111	NS	0.3747	0.4833
214342_2	F: AGTCGCATGAGATGGTCTGC R༚CGCAAGGTCTGTGTCCTGAT	272	60	C/T	72	0.1000	0.0966	-0.0164	NS	0.0905	0.0500
214354_2	F: TTCAAAATAGGGAAAAAGTAAAACAC R༚GCGCGCTACCAACTGTACTA	282	60	A/G	74	0.5333	0.4723	-0.0690	NS	0.3566	0.3667
215686_1	F: ACAGATGTCGATTCGCAGTGA R༚CCCGTCCCAAGAGTCTGTTG	331	60	A/C	55	0.3667	0.3814	0.0112	NS	0.3047	0.2500
215719_2	F: TGAACAGATGTCAATTCGCAGTG R༚TACAAACAGTTTCCCCCGCA	344	60	G/C	79	0.2333	0.2441	0.0518	NS	0.2266	0.0667
T_m annealing temperature, H_O observed heterozygosity, H_E expected heterozygosity, F_IS inbreeding coefcient, HWEP results for Hardy–Weinberg Equilibrium text, PIC polymorphism information content, MAF minor allele frequency, NS non-signifcant
P < 0.05; *P < 0.01

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published 20 Jan, 2022

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Reviews received at journal
15 Oct, 2021
Reviewers invited by journal
11 Aug, 2021
Editor assigned by journal
20 Jul, 2021
First submitted to journal
16 Jul, 2021

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Development and Characterization of 177 SNP Markers in The Mud Shrimp Upogebia Major

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Status:

Journal Publication

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