结合QTL-seq和连锁分析发掘水稻中胚轴伸长相关QTL

doi:10.3724/SP.J.1006.2021.02082

Abstract

Abstract:

Mesocotyl length is an important trait, which affects seedling establishment and early seedling vigor after dry direct seeding. Identifying the loci related to mesocotyl elongation, analyzing the genetic mechanism and selecting varieties with long mesocotyl is the most economic and effective way to promote the popularization of dry direct seeding technology. In this study, an F₂ population constructed with ‘Changai’ (an extremely long mesocotyl variety) and ‘IR 145’ (an extremely short mesocotyl variety) was used to construct long and short DNA pool, which were re-sequenced at 50×level. Two methods, ΔSNP-index and G-value, were used to identify the quantitative trait loci (QTL) for mesocotyl elongation. A QTL named as qML3, located in the region of 29.56-33.28 Mb on chromosome 3 were detected. After linkage analysis of 184 F₂ lines with the newly developed KASP markers based on this locus, the region was narrowed down to 28.89-31.03 Mb. Combining the results of gene annotation, linkage analysis, and gene expression analysis, LOC_Os03g52450, LOC_Os03g56060, LOC_Os03g58290, LOC_Os03g58300, LOC_Os03g58320, LOC_Os03g56050, and LOC_Os03g57640 were speculated to be candidate genes in this region. These genes were involved in the regulation of plant hormones as well as the mechanism of cell division. This study uncovers a locus related to rice mesocotyl elongation and is helpful for the breeding of long mesocotyl varieties.

Key words: mesocotyl, bulked segregant analysis, Δ(SNP-index), linkage analysis, candidate gene

LIU Chang, MENG Yun, LIU Jin-Dong, WANG Ya-Mei, Guoyou Ye. Combining QTL-seq and linkage analysis to identify the QTL of mesocotyl elongation in rice (Oryza sativa L.)[J].Acta Agronomica Sinica, 2021, 47(10): 2036-2044.

Figures/Tables 12

Table S1

Details for KASP markers used for linkage analysis"

Marker	Chromosome	position	Seq C	Seq X	Seq Y	Allele X	Allele Y	Changai	IR 145	Long pool	Short pool	Sequence
OS900153_K01	1	11341599	TTTCCCTTTCACTCCAAAGAAACGA	GAAGGTGACCAAGTTCATGCTTATTGTGGAAATCGCTTGACCCTCC	GAAGGTCGGAGTCAACGGATTTATTGTGGAAATCGCTTGACCCTCT	G	A	GG	AA	AA	GG	GGTGATGGCGATGCGCGGGGTCGACGGATCGGCAATGGTGAGGCGCGGGGTCAGCGGAATGACGAGGAGTGGGGGTGGCGATCAACGACGGTGAGGCGGATCCATCAGCCATATACATGTGCACACCATGTGCATGGAATCTACACCAATGTTTTCGATTTTTACTGACCTTTCCCTTTCACTCCAAAGAAACGATCTTC[G/A]GAGGGTCAAGCGATTTCCACAATAGTCTCGGTTCTAATAAGAACCGGGACTAAAGATTGTTTTTAGTCCCGGTTAAAAAAAATTTGATATTTAGTCCTGGTTCGTGATCTTTAGTCCTGATTCATCTCCTGTCAGAAGCCTGCGAGGGGGCCGAGGATCTTTAGTCCCGGTTGATTACCACTTTAGTCCCGGATGGTACT
OS900154_K01	2	8278191	TGGCACAGCCTAACAATATGATGGA	GAAGGTGACCAAGTTCATGCTAATTGCTCCAGCTTCTGTGTTGTGC	GAAGGTCGGAGTCAACGGATTATTGCTCCAGCTTCTGTGTTGTGA	G	T	GG	TT	TT	GG	TAGCAAGTTAATCTGGACAATGCAGGTTAGATCTGAAATCATTTGCTCTACAGTTTCATAATGCATATAGTTCCTTATGGTATAATATCAGCTACCAACCTGCCAATATGTTCTACAATCTCATAATGCATACAATGTCTCACAATATCAGCTGATGGATGGCACAGCCTAACAATATGATGGAAATTGTGTGGTCAGAA[G/T]CACAACACAGAAGCTGGAGCAATTTTCCTTCCACTTCTACCTTGACAGAGAAGTTCTGAAGACTGATTTTCATTCTCTGATTCCACCAGCCACTATGACAGAGCATACCTTGCTTCCACTTTTTTCCTTGATGAGGTTGTAGTGTTCCCTTCCCCATATTTTTTTGTTGTTCAACTTAAGATTCTCGCCGTTAAAAAATT
OS900155_K01	2	11054736	CCAGAAGGTTCGTTACTTCCATGTCC	GAAGGTGACCAAGTTCATGCTTGAATCCATTTATGTTAGGTGCCATA	GAAGGTCGGAGTCAACGGATTTGAATCCATTTATGTTAGGTGCCATC	A	C	AA	CC	CC	AA	ACCCCTTTTTAGTACAATTTAGAGCGCACTCACCACCATGTGTAAGCACATGCATGTCCTCTACATACTCTTGAAATAGAGGCATCGAAATCTTATAGAGTATGGTGGACATGCTAAATCACCTACTGAGTACATAATCATAAAATTGGTGGACACTAGTGCTAGATCTAGAATCTGAATCCATTTATGTTAGGTGCCAT[A/C]TCTTGTCGACCAGCTTCTGAATCTATGCTACAATAATTATTTTTATAAGGGACATGGAAGTAACGAACCTTCTGGAGTTGATTTTGTGAAAAATTTTGAACTCTAGAATTGGGTAAAATTCAGAACGGAGGGAGTATGTAAGAAATACGATAAAAAGTGTTAAAAACAACCAACGAGAATAGAAACAAGTCAGTTCAGAT
OS900156_K01	2	30473912	CGCAGGCACAACCCAGTTTACATA	GAAGGTGACCAAGTTCATGCTCACTCCATAAAGGAAACAAAATGACTTGTA	GAAGGTCGGAGTCAACGGATTTCCATAAAGGAAACAAAATGACTTGTG	T	C	TT	CC	CC	TT	GCCAACATGCTGTCGATCCTGCATGTTAGCGGACAATGCTTACAGCAGTGATTTTATGAATGTGATTATCATGAACACTTTTGATCGTCCCGGTAAGTTTTCAGATACTTGTCCAGTTATCTACATGCAAGAAAATAATTAAGTATGTACTGATTACTCAATGTACATGGGTGTGGCGCAGGCACAACCCAGTTTACATA[T/C]ACAAGTCATTTTGTTTCCTTTATGGAGTGTTTCTACAAAACCATGAACACCAATGTTTACACAAGTACAATCGCCTACTTTCTCTCCGGTCGATGGAACAGAGATAAAAGAGATCCAAAAGCACCGAGCCAAACACCAACAAAACCGAAAAAAAAAAGGAAGAGAAAAACTTTTGAATTGAACAACGTTATACTACTTGA
OS900157_K01	5	3752390	GGCACATTACCAATGCAGGACATTT	GAAGGTGACCAAGTTCATGCTACACTTTCTACAGTTGGCCTTCAGC	GAAGGTCGGAGTCAACGGATTACACTTTCTACAGTTGGCCTTCAGG	G	C	GG	CC	CC	GG	AAATCCCTACGTTTGAAACTGATTCTGCCGACAATATTAGCACCTATAGAACCATGTTCTCAATAGTGTAATATAACAATGTATAGTAGTAAAAAAAAATCAGTTTAGGCACATTACCAATGCAGGACATTTTACATGTTCAGGTGTCATTATTTAAAAAGTATTCATTTTACATATAGTAGTAGTGCTTTCGATGCATC[G/C]CTGAAGGCCAACTGTAGAAAGTGTACACTATCGTTAAAATGCCTGCTCGTGATAGTATAACTTCTAAACCTATAAAGTGATGGGGATTTTGGTGCATTCGCGTTTGGGAGGGGAGGAACCGGGATTTAAATTTGGATTTTGCAGTGAATAAAGATGTACTAATTATTGGACGAGGCATTACCAACGATCCATCCAATCTG
OS900158_K01	5	6521522	GCGTAAACCTCGGTGAATTCCTCAC	GAAGGTGACCAAGTTCATGCTGACCAACAACAATATTAGCATAGCACAAAA	GAAGGTCGGAGTCAACGGATTGACCAACAACAATATTAGCATAGCACAAAG	T	C	CC	TT	TT	CC	TCTCCGCAAGGAAAGAGATACCCTTAGTGGAAGGAGGAGTGCATTTGTGCAACCTCACGAGGATAGGGTTGAAAAAGACCCGGCTCTTTGCGAGCCCCTCAACGGAGACTAGAATCCCCTTAAGGATTTGAACTCCGGGAAATACATCGGCGCGTAAACCTCGGTGAATTCCTCACTCTCTTTACCTTCTTGTTCCATTA[C/T]TTTGTGCTATGCTAATATTGTTGTTGGTCGAGCTCACCTCTTTACTTGTGGATTGAATCTAGAGCTCTTAGGTTGTTCTCTTGTTTATATTGTTGTTGTGCAGGTCAGATAGTCTAATATCAGTTCAGACTATCCGATCACATAGGACTATCCGACCTGATATTAGACAATCTGACCCTGTTTTGTTATAGCTTCCGCAT
OS900159_K01	5	14053490	TGAAATCGTGTTAGCCGACAAGTCA	GAAGGTGACCAAGTTCATGCTGCATCTCCCAAAGAGCTAAATCGG	GAAGGTCGGAGTCAACGGATTGCATCTCCCAAAGAGCTAAATCGA	C	T	CC	TT	TT	CC	GGAGCTGACAGTCGGCAGCAAGACTAACCCTACAACATTTTTTGTCTTCGATGGGAAGGGTTCCTACAGCTTATTGCTTGGAAGGGATTGGATCCATGCCAATTGTTGTATTCCTTCAACCATGCATCAATGCTTGATTCAGTGGCAAGACGACAAGATTGAAATCGTGTTAGCCGACAAGTCAGTCAACGTTGCTAGTG[C/T]CGATTTAGCTCTTTGGGAGATGCCTGGTCTCGATTGCTTATCTGGAAAAGTTTGGGATGGAGATTTTCTAAAAGTGTCCAATTGTGATATACAACCAATTGAAGATGGAGAGCCCAAGCTTTTATTTTGAGGGTGTCGTGGAGGGTTCAAATGTCTACACCAAGGACACAGTAGATGATCTCAATGACAAGCAAGGACAG
OS900160_K01	5	21516100	CCATGGCAGTGGGTGTTGAGATTAT	GAAGGTGACCAAGTTCATGCTAATGCGGTCATGCTAGTTTTCATCTA	GAAGGTCGGAGTCAACGGATTATGCGGTCATGCTAGTTTTCATCTG	T	C	CC	TT	TT	CC	GTCAAAGGAAAATTTGCAGATGCTATTTGCTGTTCGCAAACCGAATGAACGAGAGCGATGAGCTATAAGGCCATGCCCAATGCACCACGGTGGCCAGTGGTCTCAAGCATCCACATCGGAGCTGAGCTTCCATGGCAGTGGGTGTTGAGATTATAGGCATATAATGATTTAATCTATTCCATAAATAAATCATGACATTA[C/T]AGATGAAAACTAGCATGACCGCATTATTAGATCTATACATGTAAACTACACAATATAATATGAACAGATCAAATATACGCAATATATTGAACACGTACCGAGGTGGCGGAAAGACCGGCTGCTCGGTCGAAAATTTTCGCAGGCGTCTACGAAGGCACGCAGCACGCGAGCGAAGAGGAAGATGAACCGTCGCGGACGAA
OS900161_K01	5	24914119	AGGGCACTCACACTGCGTCACTAAT	GAAGGTGACCAAGTTCATGCTGTCTAGGTGGCAGTTTTGGCTTCTT	GAAGGTCGGAGTCAACGGATTGTCTAGGTGGCAGTTTTGGCTTCTC	T	C	CC	TT	TT	CC	GAGGGGGAGAGGGGTGCCGGCGGTGGGTGGGAGAGAGAGGGGCACCAGCGGCGCAGTAGAGGAGCGGGAGCGGCGGGGAAAGGGAGAGAGAGAGAGGAGAGAGAGCGGGTGGGACCCACTGTAAGGGAAAAAGTAGACCACATGCATTGTGGAGGTTGTTGCTTACGAAGTTATTAGTCTAGGTGGCAGTTTTGGCTTCT[C/T]AAAAATTAGTGACGCAGTGTGAGTGCCCTGATAAAATCTGGCATACATGACTCAGTTGCAAGCTACTTGAAACAAGAAAATAAGAGTCGATTCTGCCTATACCGATCGTAATGACAAGACAGACAAGTCAAACACCTTGCATATAGAGGTGTACTTAGGATTTATGGTTCTAGAAAATATCATATTATATTCTAGATTAA
OS900162_K01	5	28105720	GAATTCAAATTTTCATGTTTGTGGAG	GAAGGTGACCAAGTTCATGCTCATCCCTCGATATCTTCTCGTTTGG	GAAGGTCGGAGTCAACGGATTCATCCCTCGATATCTTCTCGTTTGA	G	A	GG	AA	AA	GG	TTCAGAGCCTTTTCGCGCACTTGAATGCATATGCATGAGTTAATTTGCACACTGTGGACGCAGGGGAACACAAGAACAATGGCATGCATGCATACGTTTCGTGTAGGGCAGCTGCTGGCTAGCTTCTCCCGTACAGTGTGCTCGTGCGTGTGTGCTGCTAGCTGGGAAAGTGAAATCATCCCTCGATATCTTCTCGTTTG[G/A]TGCATGTCACCTAAATAGTCAAAAAATTATTAAAAAATTATCAACATATATTAATATGAAATATATTACTCCACAAACATGAAAATTTGAATTCAATTTCTACAAGTTGTAACAAAAATAACAAATATAGTCGAATGTGTGATAACTGTTTTCAGTTTAATTTGTTATTATTGTAGCAACTTGTAGAAGTTGAATTTGGC
OS900163_K01	7	12402368	CTCAACCTGCCTACGCAACTCTTTC	GAAGGTGACCAAGTTCATGCTGCAGCATGCAAGTCGAAGGTT	GAAGGTCGGAGTCAACGGATTGCAGCATGCAAGTCGAAGGTC	T	C	CC	TT	TT	CC	ACACCTGATTAGGGCGTTCGTACACATCCAACTGGAGAAGATCCCTGTTGTCTATTCCTAAAGAGGTATACCATGAAAGCAAACAGTGACAAGTGTGATCGTGAGACTGCAGGACCGGATGGGGTGCATGAAAATTACATAACAAACATGATGATGATTGAAGCATTTGGAGTGATGAGGGCAGCATGCAAGTCGAAGGT[C/T]GCATATGAAAGAGCTATGGTTATTTTGAAAGAGTTGCGTAGGCAGGTTGAGGAGGTACCACAAGATATTCAAGTTGTTGTTTGTGTTCTGTCTCTCAACCGCTCAAGACAAGGAAGGACAGTGTCTCGTGGGAATCAGGGGTAAGGGTAAGCCACCGTGCCAAATTTATTTGATTTGAGAGAGAGTACACATATCTTCTT
OS900164_K01	8	28356273	AACAGGCCGAGGCTCTTCACCTACT	GAAGGTGACCAAGTTCATGCTACTCCCTAGTTCCCAAACACTCTCA	GAAGGTCGGAGTCAACGGATTACTCCCTAGTTCCCAAACACTCTCT	A	T	AA	TT	TT	AA	ATATATATATATATATATATATATATATATATATATATATATACATATATATATATATATTTGTTGGATTAATTAGTAGTAGTTGATTTATGGGGTGTTTAGGAGAGAGGGGCTAAACTTAAAAATATAAGTCTCTAGAGTAGGGACTTATATTTTTAAAAAAAGGGCTAAAGTTTACTCCCTAGTTCCCAAACACTCTC[A/T]TAGATTAGCTAGTCGATCGATCGGCTTACTGTCCAGTAGGTGAAGAGCCTCGGCCTGTTGTCCCCATACAGCTCAGGGCTGACCTGACTACAAGGAAGGAAACATGCAAATGCTTCAGATTCAGATTTAGATCCAATTATATATATGCTCAGCTCTGCTCAATACTACTACTAGTATGAATTAATACTCCTAGGAGTATA
OS900165_K01	9	19464447	ACGGGATATGTGGTGGGACCAG	GAAGGTGACCAAGTTCATGCTTGTATAAATTGCGAGAATGCTCAACG	GAAGGTCGGAGTCAACGGATTTGTATAAATTGCGAGAATGCTCAACT	C	T	CC	TT	TT	CC	CGAATACACTAGGTGAAACATTTTTTTATGAAAAAAAACAAACCAAATTTCCTTAATAGATGGTTTCCAAAATATGTAGGTGATTTGTTTTATATGGATAAGTGACAGGTGGGGACACGGGATATGTGGTGGGACCAGGTGGGCACGTGATGGGGGGAGGGGGGAGCGACCGATTTTTTTCCCCTCCCCCGCGCGCCCGA[C/T]GTTGAGCATTCTCGCAATTTATACAAGTTGAATTTTCAACCTGTCTGTCTGTGGAACGCTATATTTCGTATTAATCATCTTATTAATTTTGGTCAACTTACAATAAACGAGTGGATTGTTCATCAATCCCTCTCCGGTGCACATGCTATTTAGATTCCGACGTGGACGGTGCACGTCCAGTCGTCCACCACCACCACCAC
OS900166_K01	10	180016	CGATAACCTAGGATGATGCACTGCTG	GAAGGTGACCAAGTTCATGCTAAGGCTTGCTCGGCAGTTTTA	GAAGGTCGGAGTCAACGGATTGTAAGGCTTGCTCGGCAGTTTTT	A	T	TT	AA	AA	TT	CGCCTCATCATCCAATTCTATGTGGCATTTTTAGGGCAACACATCAAGTATCATATAGTACTTTGCCCTTAGTTGCTATCCTATTGGATGTATATGCCAGAGTACCATATCATTATCTTGAAATTGGGATGTCTATAAAAGTAGATGGTGTTTCTCATGTCTGACACCTATTTCCCTGGTAAGGCTTGCTCGGCAGTTTT[T/A]CAGCAGTGCATCATCCTAGGTTATCGAACTGTCGACAATTCTGAAAATAATTGATCAGCTATGGATCATGTGTTTTTCTGTGCGTGCGGTCTTGCGATAGCTTCTTTATACGTTTGATCATAACCTATATAAGATGTTAGAATGAAGGAATTCAGTATGATTAGTGACATTGCAGTTGAATTGTAATAAATAAAGATGCA
OS900167_K01	10	4232779	TCGAGGTTCGACACGTTTATAGCAA	GAAGGTGACCAAGTTCATGCTGTTCTCTTCAGGATGCTTGTCGTGT	GAAGGTCGGAGTCAACGGATTGTTCTCTTCAGGATGCTTGTCGTGC	T	C	CC	TT	TT	CC	ACCCAAGAAGTCAATAAGTGGAGTTCGCCAGTCTTTCATTGTCTTGATGTCAACAATGACATGTTCGACCTCTTGAGCCCCCGAGGAGTTGTCGGTATTGGCCATGGTACCTTCGTCGTGCGACTCTTTTACAGACGGTTTTGTCAGGACATCTAAGAAAGTTCCTAGTTCAAGAGGTTCTCTTCAGGATGCTTGTCGTG[C/T]TAAGTCATCTGGTTCAATGTTATCCTTGCTATAAACGTGTCGAACCTCGATGCCGTCAAACTTCTGCTCTAGCTTCTTGACTTCAAAGAGGTACTTAGCCAACTCAGGATTGGAGCATTTGTAATCCTTATCCACTTGGTTTGCGACTAATTTTGAGTCCCCTCTCACAATCAATCGTTTAACTCCTAGTGCAACGGCTG
OS900168_K01	12	2919839	TCGTTTCGCAATCAGTAGGAGGAAA	GAAGGTGACCAAGTTCATGCTGGGTGGTGTCAGATTCACTACTCATT	GAAGGTCGGAGTCAACGGATTGGGTGGTGTCAGATTCACTACTCATC	T	C	CC	TT	TT	CC	CCACCATACACTTTAAAGCCTAAAAATTAAAATAAAATTATTCTCAATGTAAAATATTCAGGTCATATTATTTGTCATTATTTTTACTTTACTTCAAAAGAAATTGATGGTTCGAGGTTAGGGAAATAACAAAAATCCACTTAACTTTTCGGAGAATCCATATGACAGTGGTGATGGGTGGTGTCAGATTCACTACTCAT[C/T]ACCACTACGTACTATTATAGAAAAGCACTTCAAGTAGTACCTACATTTTTCAAGTTGTAGCTAGATCTTTTTACGAATTTGAACTTTCCTCCTACTGATTGCGAAACGAATTAACCGGCCACCGTACAAACTTTTCATGGTACAGGCATGCATGCTTCTTGATCCTTTGCATTTCAAATCATGGTGTTTATGCCGTGTAC
OS900169_K01	12	7367534	GCTAGCACATATGACTGATGCATTACA	GAAGGTGACCAAGTTCATGCTGAGTAGCTGGTGTATTTTTCAGTGATT	GAAGGTCGGAGTCAACGGATTGAGTAGCTGGTGTATTTTTCAGTGATA	T	A	TT	AA	AA	TT	TTTAATTAAATCTAACATTGAATATATTTAAATAGTATGTTTGTTTCGCATTACAAATATTATTATGTAATTTTTAATCTCGGTCAAACTTAAAAAAATAACTTAGAAAAAAATCAAAGAATTACCATAATTTGGCTAATAATTAGTTTTATTTTAGTATGGTCAAACTATTTAGAGTAGCTGGTGTATTTTTCAGTGAT[T/A]CTCTTGTAGAGTAGGATTGTAATGCATCAGTCATATGTGCTAGCTATACTATTGAATAATTGAATGTGGACCGATGTAGTTTATAGCATTGTAAGGGTTATGGTTTACGTCATATATCACATGAAGGAAATGAAGATGACGCAAACCAAGTTGATGGATTGCGTCTTAGCAAGAACGACCAAACTTATCATGGTCCATCC
OS900170_K01	12	27253671	TATAACAGCGACCACCCAGATGACC	GAAGGTGACCAAGTTCATGCTATCACGTCCCCCGTTGTCA	GAAGGTCGGAGTCAACGGATTATCACGTCCCCCGTTGTCG	T	C	CC	TT	TT	CC	CAGAGGGAGGTTCGCGACCAAGGTAGCAGAACGGTGAGGGACGCCATTGGCCGAGACGGCGGAAGAAGGCAAGAGAAGGGGCACCGCGACAGGCGCCGGGATGACCGCGATGACCGTCGCGGGCGCAACAGGAGGTATAACAGCGACCACCCAGATGACCTCCGACGTGGAGGACGGCGCGACGACGACAATGATGATCG[C/T]GACAACGGGGGACGTGATGTCGCGCACGGAAGGGGCGGCGTTCGCGGCCCAGACGTCAACTTCAGGCGGGAACGCACGCACTCGCCGCGTGCCCGCGATCGCGGCGACACGGGAAGACGCGACGGGCAACGCCATCAAGCAAACTGCGGCGGCAAGGACGACGGGGCCAACGACCGCGACATGGGCAACCCACCCCCAGC
OS900129_K01	3	28890281	GCTCAGATTACTGGCTGTGTCA	GAAGGTGACCAAGTTCATGCTCATCGATCGGTGTCATTCA	GAAGGTCGGAGTCAACGGATTCCATCGATCGGTGTCATTCT	A	T	TT	AA	AT	AT	AAATTGATCATTATGATTTTTTAAACAACTTTCGTATAGAAGCTTTTTACAAAAAGTATACCGTTTAGTAGTTTGAAAAACGTACGCGCGGAATACGAGTGAGAGAGGTTGGGAACAAGAAGCAACAAACATAGTACGCGTCCTATACCCCGGTGACCTCTATATATACCGTACCCCATCGCCATCGATCGGTGTCATTC[A/T]TTCTAAGCTTGACACAGCCAGTAATCTGAGCTAAATTAGTCCTAAACTCCAAGTTGATTATCCAACGAATCGTAGCCTCGAGGGGGTATCTGAATCTCCAACCACTTCAATTCAACGCGTCGCCATCGCCATCTTCGTGTAGAGGCGACCTCACCTACGCGCGCGGCGCGCCCCTGGCCATGCAGACGATAAGGTGGTCG
OS900130_K01	3	29290258	TGCATTATCCTCGAAAAACAA	GAAGGTGACCAAGTTCATGCTAAAATTGTAATTGGTTGGGAAGAA	GAAGGTCGGAGTCAACGGATTAAAATTGTAATTGGTTGGGAAGAG	T	C	CC	TT	TC	TC	GAGAGTCCACATAATGTGTAAAAAATGTGCATGTTCCCTGCAAACTTAAGGTTCAACTTTACTTATGCGAAATTGCGGATAGGAAAAAAAAACTGTTTCTACGGATCGCAAGACTATGCATTATCCTCGAAAAACAATTTATACCTTGCATTGTAGCATTTAGAATTTGTTCCAACATATAACAACTTTATATTTAAAAT[C/T]TCTTCCCAACCAATTACAATTTTCCACCATTTATTTATTTTTTCATCCACTTCCTCTCTCCCATGTTTACTTACATATGTTTTTGATAACCATGTCCAATCTCAAAACTTCTTATCTTTTAAAACGGAGGTAGCAAGGCACATTCTTCTCATGATGTTAGATCGTCTTTCCTCATGTAAACAAGTACCATGGACAGTATC
OS900131_K01	3	29692468	GCACAGACATCCTCGTGTCA	GAAGGTGACCAAGTTCATGCTAATCTTTAAATAGTTTCTTCTTTTCTTCTTCT	GAAGGTCGGAGTCAACGGATTTCTTTAAATAGTTTCTTCTTTTCTTCTTCC	T	C	CC	TT	TT	CT	CGCAGGTCCGGGATGCCGCCGACCATATCGTCCACAGCTTCGAGGGTTCGGCCCCTCGGCTCGCGTTCGCCCTCAACTCCGACGAGGAGGGCGATGACGGCGGTGTGGGCGACAGTGGCGACGAGGCTGGCGACCCGGGTGCATCGGAGTGAGCCCCCAGGCCCCCGCCAATCTTTAAATAGTTTCTTCTTTTCTTCTTC[C/T]GAGGCCTTCGGGCCCCCTTCTTGTATAGACTAATTTAATCTGCAATCAAATAAAGAGGAAATTTTTTGTGTCAATTCTATTTGTTGTGTGTATGACACGAGGATGTCTGTGCCGCGGTCCTTTTGTGTCTTGGCTTGAACAAGGGCTCGTGCCCAGGTCCTAGTCCTCAAATGGCTCGGGTCGGGGCTAGTGCCTGGGGA
OS900132_K01	3	30106408	CCACTAGCGAGTAGCGAAGC	GAAGGTGACCAAGTTCATGCTATGGCCATGGTGAGCGTT	GAAGGTCGGAGTCAACGGATTATGGCCATGGTGAGCGTC	T	C	TT	CC	TC	CC	TTATCGAATCGCCACTGAAGTTGATGAGCTGGCTCCTCCCGTCGTCGTCGGTCCAAAGAGATAAGACGGAGACCTCACTCCACACGTCGAAATTGGCAGAGCTCAGATTGGGCGTCACCGCACAGGGGAGCGAGAGTGGAGGGAGGCATGGGGATCATGACCTTGTACTCCCACTCGAGGCGGATGGCCATGGTGAGCGT[C/T]TGCGACTGCAGCTTGTACGGATGCTTCGCTACTCGCTAGTGGCTTGAGGGTGCGGTAGCCGAGCATAACTGATGTGACCATGGCTACCACGGATGCAACCATTGCTCACATCATGGATGAACAAGAAGATATCAAGATCAAGTACTCCAAGTGCTAGAATCCGATTCGGCCACCTACTACACTGCTGACTTCAAACGGCC
OS900133_K01	3	30372501	GCTCCACCTTGAAAGCAATG	GAAGGTGACCAAGTTCATGCTTTTCTAGCGTGGTGGAAGAGATA	GAAGGTCGGAGTCAACGGATTTTCTAGCGTGGTGGAAGAGATT	A	T	TT	AA	AT	AT	ACTTGTTGTCCATTTCCATCGTATGTTGTCTTCAATGTCTTGGGTTAGTGTGATGCCTGAGGTCCAGATTATCTCGAAGACCTTGAAGAAATCGGTGACGAGGACAGTTGTCAAGTTGTATCGGATGTCATCGATCCACTTGTTATCTTGTAGGGCTTCTGCGACCGTCCTTTTCTTTTTTCTAGCGTGGTGGAAGAGAT[T/A]GGGTGCCATTGCTTTCAAGGTGGAGCTGCAAGCCCATGGGGATTCCCAGAAGAGCGCCTTCCTACCATCTCCGATTGTCACTGACGTGGATGCTGCAAAGAGCTCGTTGTCCTGTTCATCACAGGGTGTTGGCATGCCGATCCATGGCTTGTCGGGGGAGGTCCATTCATACCATAGCCATCGCAGGCGAAGCGCCCTTC
OS900134_K01	3	30668336	GCCTTGGTAGCTCGGAAAA	GAAGGTGACCAAGTTCATGCTAGATTCGATGTAAAGTTGAGGGAC	GAAGGTCGGAGTCAACGGATTAGATTCGATGTAAAGTTGAGGGAT	G	A	GG	AA	GA	AA	GGGACTACCCTTAGCCCGCTGTACCTGCTCTTTCCTTGCCCTGCCCTGCGCGGCCTTCTTTTCCTCCCAGCCCCAAGCTCTTCTACGCGGTCCGTTTACTTGCTTGGGATCCTCCCAGGCTCCCAGGCCATGTCTCATCTGTCCGACTGTCCGCGCCCTAATCGCCTTGGTAGCTCGGAAAAAAAATAAGTTCAGATACC[A/G]TCCCTCAACTTTACATCGAATCTGTATGATATCCCCAATATCAGATAGGGTTAATTGGATCCATGCTATTATAACTTTACCACTTTTCCCAAAAAAAAAAAACTTTACCACTTTTGATAAATGCTACTACTATTTGTTGAATTGCAAACATGCCATTATAAATCAGCTAATTTTGGAACCATGCCACTCTCTACATCCTG
OS900135_K01	3	31027370	ACTAGCCCCACACAGACCAC	GAAGGTGACCAAGTTCATGCTGGATTTTATGGGCTTTTCCA	GAAGGTCGGAGTCAACGGATTGGATTTTATGGGCTTTTCCG	T	C	TT	CC	CT	CT	TACGGGGGAGATGCAGCCTGAGTCCGTCCTGATTCTAGGAGACGGTATCCCGTCCTTCCCGTTTCACGTGCACCAGCTGCGAGGGGGAACGCCCGCTGCGCGCGGGCAAAATCGCTCGCTTGCGGCCTTCTGGTCCATCATTCGTACTAGCCCCACACAGACCACAGCGGCGGCACGCTGCACGCACGCAAAATTTCCAC[T/C]GGAAAAGCCCATAAAATCCAGGAAAACGTGGTGGTTTTGCCAACCTCCCGCCCCTCGTCCAAAAAAAAGGCCCGGAAATAAAAGCGGATTGGAATCTGGTGGCTCCGGGTCCGTGCGGTGCGGGTGCGGCTCGCTCGACTTGGCGTCGTTGGAGTCCACCTGACCTCCTGTCCTCCACCGCCCGCTTCCCCTCGCCTCGG
OS900136_K01	3	31391306	GGAACGATGTGACGGAAAAA	GAAGGTGACCAAGTTCATGCTGGACTTCGTCAAACTTCCAAC	GAAGGTCGGAGTCAACGGATTGGACTTCGTCAAACTTCCAAA	G	T	GG	TT	GT	TT	AGCCAAAAGGTTTATATTTAAAAATACTTTAGAAAAAGACTATTAATAAAATTAAAAATAAAGAGTCTAAAAAATAAAAATATTTTTAAGTTTGGATGTGTTTGCTTCATGCTAAAATTGGAAGTTTGGTTGAAATTGGAACGATGTGACGGAAAAATTGGAAGTTTATGCATGTAGAAAAGTTTCGATGCGATAGAAAC[T/G]TTGGAAGTTTGACGAAGTCCGTGTGCGTCACCGACATATGGGTCCCTTCTAGCGGTGCAGAAAGTGATAAGGTTCAACCAAAGTCGCAAGTCCGCAACGCGACTGTGCACACGAGGCCACTCCACTCCTCTCCTTTGCGCTCGCTCTGCTCTGCCATGGCGGAGGCGCTCGTCGCCGTCCTCCGGCTCGCGGCGTCCGCC
OS900137_K01	3	31783291	CCATGGACTATATGGGGTGTG	GAAGGTGACCAAGTTCATGCTGTTTCACAAAGCAACACAGCAT	GAAGGTCGGAGTCAACGGATTTTTCACAAAGCAACACAGCAC	T	C	CC	TT	TC	TC	TGCAAGCTACTGCACTAGGAAGTATGTAATCTGGTGAATGCAAAGAGTACAAAGATTGTTTAAGCATGCACACTCATTACCTGAAGATTAGGAAAGGCAATGGATGAACAAAAGGCTCGGGAAAAGGTTGCTTGGAGCAGGACCGCATGAAATTGACTCTTTCTGTTACTTCCATAAAGGTTTCACAAAGCAACACAGCA[C/T]TAGTTGCTCACACCCCATATAGTCCATGGCTCCATGCCTTGTCTCGCCAAGATTGCCAGCTTCTGCACTGTTATCTATAACAAAAAACAGCTTCCATATTAATGTGTCGCTGCTGATTTTTCTTTTTAACATAACATAAGGATAGAAGATGTGGATGTAGAGCGAACAAGAAGCAAAAGGGACAGACCGAACAACACGTT
OS900138_K01	3	32205877	AGGAAAGATCTGGCCTTGTG	GAAGGTGACCAAGTTCATGCTCGAGTGATCGGCTGTCTTT	GAAGGTCGGAGTCAACGGATTCGAGTGATCGGCTGTCTTC	T	C	TT	CC	TC	CC	CCTCGGGATTGAAGTTGATCAGGGAGAAAATGGAACCACGCTCAAGCAAACTGCCTATGCCAGAAAAGTGCTTTCTCAGTTCGGGATGCTGGAGTGTAATTCAACCTCAATTCCGATTGATCCAAGGATGCAGCTGAACAAAGATGCAGATGGTCACCCGGTGGGATGTAACTGAGTATCGGCGAGTGATCGGCTGTCTT[C/T]GATATCTGTTACACACAAGGCCAGATCTTTCCTTTGCTGTTGGAGTGGCAAGCAGATTTATGGAGCGGCCAACTCTTATGCACTTCAAAGCAGTGACACAAATTCTCAGATATCTGAAAGGTACAATTGATTGCGGCCTTGTGTATGCAGCTTGAAATGGTGATATGCAGATTACTGGGTATACAGACAGCGACCCGCTG
OS900139_K01	3	32341783	GCATTGGGTTTGTTGCTAGA	GAAGGTGACCAAGTTCATGCTCCAAAAAAAGCTAATAACTCTCTCATATTT	GAAGGTCGGAGTCAACGGATTCCAAAAAAAGCTAATAACTCTCTCATATTA	T	A	TT	AA	TT	AT	GGTGATGAGGTGGAGGAGAGAAGTGAGGACAGAGATGATGAACCACCCCCCACACAAACTTCAAGAAGGATGTGAGAGTACTAAAGTCATTGATATTTGTGTATTAGAGGTGACCTATTGTATACTCTCTCCATTCCAAATTGATCTACATATTTCATAGGTACACCAAGACCAAAAAAAGCTAATAACTCTCTCATATT[T/A]TATTTACTCTAGCAACAAACCCAATGCATGCACCATCCCCACTATTTCCTAGCCAATAGCAAATTAAGATATTGCATGTGGGTTATAAATACTTGTGTGCATGGATGCATGCATCAATGTCCATTTACTCCAATGGACAAATAACGAATAGACTTAATAAATAAACACAAATATGTAGATCATTTAGGAATAACCTCAAA
OS900140_K01	3	32789243	GAGACAGCGTGAGATTGTGC	GAAGGTGACCAAGTTCATGCTTCCCTTCTTTTTTTTTTTCGTTACT	GAAGGTCGGAGTCAACGGATTCCCTTCTTTTTTTTTTTCGTTACC	T	C	TT	CC	TC	CC	ATCCTTCTCGTCGTCTGGGAGATACAGAAGAAGTGGAACCAACGAATTTTTGAGCACAACGAGAGCATGACAATCACCCTCCTAGCAAAAATTAAGGAAGAAGCCAAAATTTAACCCTAGGAGGAGCTAAACCACAGTTAATTCCTAAGAGCGTATAATCTGTAAAGACGGGCTTTTCCCTTCTTTTTTTTTTTCGTTAC[C/T]AGGGGTGTATTTTTTTCCTCTCTATCTAACGAAAGATAAAGCACAATCTCACGCTGTCTCCTTTTAAAAAACACTTTCTTTACGCTGTTCATTGGCTGTAGCGGGTAGAATTCGCAAGGAATATGAATTAAATTTGGTTATAAATGAACGTACTTTTGTAATCACAACAAAGGGTCCATAGCTCAGTGGTAGAGCAATTG
OS900141_K01	3	33203208	CGCATAACCCTGATGGAGTC	GAAGGTGACCAAGTTCATGCTCTCGCTGTGAAGGAGACGA	GAAGGTCGGAGTCAACGGATTTCGCTGTGAAGGAGACGG	T	C	CC	TT	TC	TC	TACCTTGCTTTCCTCGATCGGAGCGCCCAGAGTGACCAGCGTGGTGACCAGGTTGTTGAGGCGTAGCGAGAAGTCCTCGACGGACTCCCCCTCCTTGAACTCGATGGCGTCGTACTGCCGTAGAAACAGTTGCGCCTTGGACTTGCGCACTCGATCAACGCCGACTCGCATAACCCTGATGGAGTCCCACGCCTCCTTTG[C/T]CGTCTCCTTCACAGCGAGCGTCAACAGCATCTCCTGCGGCACTGCACGGAGGATGGCCTCCAGCGCCATTCTGTCTTCCTGAAAGTCTGCGTCGCCGTGCTAGACGGCTTCCCACAGACCACGGGCTTGGAGCATAACTTTCATCATCAGGGACCAGTCACCATAGTTTGTCTTCGTGAGGGTAGGATAGTTTGCTGAGC
OS900171_K01	3	14489983	GGTGACCTCGATACAAACTCGGTGA	GAAGGTGACCAAGTTCATGCTCTTCCGTATGATTTTTCGTCTGTCA	GAAGGTCGGAGTCAACGGATTCTTCCGTATGATTTTTCGTCTGTCG	T	C	CT	T/C	CT	CC	ACGACGGTTGGTGGCGGCCCGGAGGAGATCGGTAGTGGCCACTAATTGGGAAGGGGAGGGAGCACGGGAAGAAAGGTGGGAGGTGGAAGAGATTAGGAGAGGGAGTGCGTGCATGAATCAGGGGATGTGATCAAGGGACCGTGATTAGGGGATCCAGATCGCTCTCTCTTAAAAGGGTGACCTCGATACAAACTCGGTGA[T/C]GACAGACGAAAAATCATACGGAAGCCTTACGTATGTTTTAAGTAGGTATAGATGTCATGTATCCTATAGATACAGATCTACTACTACGATATGTATTTAATATTTTAATATGTGACCAAATGTTATATTTTTGGGACATGTTTTGATATATCCAACTGATATGCAACTGATCTATGCAATCATTTAAAGTATGATATAAT
OS900172_K01	4	35335719	ACGGGCTGCTGGATTTACATAAGGT	GAAGGTGACCAAGTTCATGCTTGCTTCAAACATATATTCATAGAGTCG	GAAGGTCGGAGTCAACGGATTGCTTCAAACATATATTCATAGAGTCA	G	A	GG	AA	AA	GG	TTTTGTAACCCTGGAAACCGCGAGACGAATTTATTAAGCCTAATTAATATGTCATTAGCACATGTAGGTTACTATAGCACTTATGGCTAATCATGGACTAATTAGGCTCAAAAGATTCGTCTCGCGATTTCCATACGAACTGTGCAATTAGTTTTTTATTTTATCATTATTTAATGCTTCAAACATATATTCATAGAGTC[G/A]ATGTGACGTTTTTCGGAAAAAAAATTAGGAACTACACAAGACCTTATGTAAATCCAGCAGCCCGTACTATTCGGGGATGACAGAAGGATGTCGATCTACACGGTTTATTAACAAGCTTTGGAGTTAAATTTCACCATTTAGCATTTTACCTTGAGCATTGGGAAAAGTAAGAAAACCCTTCGTGCAATGGAGAAATTCAT
OS900173_K01	6	29173606	AGCACAAAGGGAGTTGACATCATCA	GAAGGTGACCAAGTTCATGCTGTCCTGTATCAAGTTTATTTTTAACA	GAAGGTCGGAGTCAACGGATTGTCCTGTATCAAGTTTATTTTTAACG	T	C	CC	TT	TT	CC	TAGATAGTGCATCTACACCTTTCGAATGAGGAGGAACAGCCTCTGGTCCAGCTCAAAGCTAGCGGCACTGGAGGGGTCACCCTTGAGCATCATCAGAAGGCCACCAAACGATGCATAGATCTCCCTAGAATGGAAAAGAATGCAATTCATTAAAATTCATAGCACAAAGGGAGTTGACATCATCACATGATACAGGATTA[C/T]GTTAAAAATAAACTTGATACAGGACTAACAGTAGTCTAGTACAAGCTGTGTAGCTGTAGGCCAGATTTACATATTGGCAAGGCGAAAAATTGTTCTTTGAAGGTACTTATCTTCGTATAACATGATTCACATAACAATGATACAATTAATTAAGTAAATGCACTTGAATTGAATTAACCAAGTAGCTGAAACAGTACAGA
OS900174_K01	7	23668282	AACATCTTCAGCCCTTGCAACCCTA	GAAGGTGACCAAGTTCATGCTGTTCATGTTGTTGCTGGTGGGTCTA	GAAGGTCGGAGTCAACGGATTGTTCATGTTGTTGCTGGTGGGTCTG	T	C	CC	TT	TT	CC	TATTTCTTGTTCATTACATGATCAAATCAACTGGCACGCTCATACATTCGAAGGCGAGCTTTGGACCTGCACTAGAGTTAAACAGATCTCCCAGGCCTCGTGTTTTCTGTCAACAACAACACCAGCCCCAATGCCTACACCATCTTGACCAGCACCAATTGGAACATCTTCAGCCCTTGCAACCCTAGCATTCTCAGCCT[C/T]AGACCCACCAGCAACAACATGAACTTGGGCTAGATATGGGATCTCATTCTGTGGACGGAACTGAAGAAATAAAAAGATGAAACATAGTCTTAGTAAGTGGTGAAACACAAAATGTATATATACTAAAACATTCATAGTTGTGAAACATACCGGGCGAGACCCATATGTGACATAGCCAAGGTTCATCCTACAACGGTCTA
OS900175_K01	9	6324514	GCATCTCTTGACCCTATAAAATTGA	GAAGGTGACCAAGTTCATGCTATGCAAGCAATGTGATTGGGAGA	GAAGGTCGGAGTCAACGGATTGCAAGCAATGTGATTGGGAGG	T	C	CC	TT	TT	CC	TAGAAACAGAAAGTTGGGGGACTCAACATACCGAGTACATCGACATAAAAACATAATCTCAATACTCCCTCCATCCCAAAATATAAGGCACAACCATTTTTCTCTCATGTCACATAATATAAGGCGTGTATGCATGTATATATTAACTAGCATCTCTTGACCCTATAAAATTGATTTGTTTTAAATCTTATACCATTAAA[C/T]CTCCCAATCACATTGCTTGCATGCATCCAAGTGATCCAACCATGAAGATGATAAAATATTTTCTTGGTCTTTGTGTTTTGAGTGTTATACCTTATATTTTAGGATGGAGGGAGTATTAAACTATACTAAAATACTATTAGGAGACCTTTAGCACCTCCTATCTTATCAACTATGACGAAAAATTTGAAGGGGGGACTCAG
OS900176_K01	9	10024501	TCGGATGTTACGTGTGTATGCAACC	GAAGGTGACCAAGTTCATGCTTGGACCTCATATTCATGTTGTTTGGT	GAAGGTCGGAGTCAACGGATTGGACCTCATATTCATGTTGTTTGGC	T	C	CC	TT	TT	CC	TCTGATAGGCCACTTTCCGGATAATCCGAAATTATCAACATATGTGATATCTCTATCTATTGCATATAACATAAATTGGTTCCTTCAATGATCTAATTCATCAATTAACCTAGATTTCTTAGTCTGAGGCTTTCACCGTTTCTTGTCAGACTTGCCTAGCTGTATTTTTATATTATGGACCTCATATTCATGTTGTTTGG[C/T]ACTTAAGCATATAATTATTACGATGGATCGTTTATTGATTATTATATTATTGTTCATTGCATTACTAACTTGATATTATATTGGTTGCATACACACGTAACATCCGATAAATTTATTCCATTCCCGAACTGATTCCGCACCATTTCCGACATCCAAAATAATCCGTTCCGCATCCGCGTCCGTACACTATCCGCACCCGC
OS900177_K01	9	15799081	ACTAGCTTTCGTGCAAGGATCAACG	GAAGGTGACCAAGTTCATGCTCCAAGGTACGTTATCTCCTTTAGTTG	GAAGGTCGGAGTCAACGGATTCCAAGGTACGTTATCTCCTTTAGTTT	G	T	GG	TT	TT	GG	CAGATTGTCTTGAATGATCCTGTTGAGAAGTATATGATTCCATTTCAAGAAACCCAGCCATTGCATGCTGACTTAATCTTGGAGGAGGTTGTCATGCGATTCTTCAAGGATCCTGTAGTTCCTATTGTTGATGACTGGGGAAGCTGCGTGGGTATTGTTCACCGACAGGATTGTACCAAGGTACGTTATCTCCTTTAGTT[G/T]GTACCAGCAATAATAGCGTTGATCCTTGCACGAAAGCTAGTGGAATGGTTAGCACTTGTTTTAGCGGCAGGGACCAGTCACCAGTGTTAGGATAAAAAAAATCAACCACCTTAGCTTCTCTTCCAAACAGTTCAAGTTTGGTCAAGGATTATATTACAAGGAGGAAACCAATAACAAATTTTGGTCGTTTTTCATTTTCA
OS900178_K01	10	8923315	CAGACATGGGGATGGATGCATATAGA	GAAGGTGACCAAGTTCATGCTTGCAAAATAATGAAGAGATACAAGTGGAAA	GAAGGTCGGAGTCAACGGATTTGCAAAATAATGAAGAGATACAAGTGGAAG	T	C	TT	CC	CC	TT	TAACACAGAAAGTGAAAGTATATCTATCTATTTTTTTTGATCGAGTTCAAATTTTGAGATTACTGTGCTTGTCATATCAATATTTCAGGAAGATATTCAGCTTATGGCAGACATGGGGATGGATGCATATAGATTCTCAATTTCATGGTCTAGGATTTTCCCAAGTATGTAATATAATAATTCATTGGTTAATATGGGTA[T/C]TTCCACTTGTATCTCTTCATTATTTTGCATCTTTATGTTAACTTAATGGTCACACATAACCTTTGAAGTTTTTCTTCATTATGAAATGTTTTATCTGTGGATAAACAGACCTGCACTACTAACAATAATCATATCTGCACTCTTATTCAGATGGCACTGGTGAGGTCAACCAGGCAGGCATTGATCACTACAACAAGCTA
OS900179_K01	10	12020045	TTCAAGTTTTAGTTTGGACACTCTG	GAAGGTGACCAAGTTCATGCTCAGCTGGTGAGTTCAAAGTGAAAAGATA	GAAGGTCGGAGTCAACGGATTGCTGGTGAGTTCAAAGTGAAAAGATG	T	C	CC	TT	TT	CC	GTCACGCATGAAGTACTATTCACATTTTATCATCTAATAACAATAAAAAATACTAATTATAAACAAATTAAATAAGACGGTGAAACGTTGGACATTGAAACCCACAACTACACTTAAAATGATACGGGGAAATAAATTGAGTAAATTGCAATTTGGACCATCTTTTATTATTCAAGTTTTAGTTTGGACACTCTGTATTT[C/T]ATCTTTTCACTTTGAACTCACCAGCTGATCAGAGTTGCGCTTAGCCATCGTTGTAGTTTTTTTTTCTCCTTTTCCTTGCTGCAGCTTTTGTTTTGCTTTTTCTCTCTTCCCCTGGTTTGGTTTGGACCGGTCTGCGGGTGAAGTAAAAAGATGACCGGTCTAATTAAACCAGGGAAAGGGAGAAAAAGAGTTTTTGTTAC
OS900180_K01	10	22817323	ATATGAATGTTGTGCCGGTGGTGAC	GAAGGTGACCAAGTTCATGCTGATGACTCCCTATGTTAACCGATCCT	GAAGGTCGGAGTCAACGGATTATGACTCCCTATGTTAACCGATCCC	T	C	CC	TT	TT	CC	TTTCCATTCTCGCGAACCTTCCACACACCGAGAGCTTAGAATCTCACCCAGGGCCCCCGGCCGAACCGGCAAAGGGGGGCCTGCGCGGTCTCCCGGTGAGGAGCCTCACGCTCCGTCAGGTACACTAGCCGGTTTTGACAAGTCTTAGCTTAGATCACCGCAATAATCTTTAAGGGATGACTCCCTATGTTAACCGATCC[C/T]GCCTCAGATCCGCGCTCGTCACCACCGGCACAACATTCATATCCGGCCGATATGGCGATTTAATATATGCTACTATCTTCCTTCCAAAATATAAGGAATATAAGGAGTTATATTTTGAGATGGAGAAAGTACTAGTGATGATGAGGAAGATACACTAGTGCTTGAAGGCTTAGTTGTTTTGTTCTTTTTCCCAACTCACC
OS900181_K01	11	11901489	CATTAGGGGTAATTCCATTGTAGGG	GAAGGTGACCAAGTTCATGCTGACTACCTATTATTGTTTTCAGTCAATTCT	GAAGGTCGGAGTCAACGGATTCCTATTATTGTTTTCAGTCAATTCC	T	C	CC	TT	TT	CC	CTCTCTGGGTCCATCCATAAGCATGCATACTGGCGCTCTCTTATTGGCTATACACACACACACACACACATATATATACATATATATATATATATATGTGTGTGTGTGTGTGTGTATAGTACTTTTAGATTTGATTAAATTACTTCCTATACATTCATAATGCTACGAGGTGACTACCTATTATTGTTTTCAGTCAATTC[C/T]GTAATTTGTGCTGATTAATTTAGTTTCTAGATAGAGTTATGTTTTTATCCCTACAATGGAATTACCCCTAATGTTATGACAAAGTTACTTTCGTTTTGTCTGAAGTTACTTCTATAATATATGTAAATTACATTTAAACTTTATTAAATTTACTTTTGTATGTCTAAGAAGTAATTTAGTGATATCCAAAAGTAATTTAG
OS900196_K01	1	38383221	TAGTAGTTGCACCGCATGATTGAGC	GAAGGTGACCAAGTTCATGCTGGCGTGGAGCGAGGCTACTAT	GAAGGTCGGAGTCAACGGATTGGCGTGGAGCGAGGCTACTAC	T	C	C		T		GATGAAGGAGCTGTCGCTGACGATCATGGAACTCCTGGAGCTGAGCCTGGGCGTGGAGCGAGGCTACTA[C/T]AGGGAGTTCTTCGCGGACAGCAGCTCAATCATGCGGTGCAACTACTACCCGCCATGCCCGGAGCCGGAGCGGACGCTCGGCAC

Table S1

Table S2

Fig. 1

Fig. 2

Table S3

Fig. 3

Fig. 4

Fig. 5

Fig. S1

Table 1

Table S4

Table S5

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基因名称Gene name	起始Start(bp)	终止End(bp)	正向引物Forward primer(5'-3')	反向引物Reverse primer (5'-3')
β-Actin			AGTGTCTGGATTGGAGGAT	TCTTGGCTTAGCATTCTTG
GAPDH			AAGCCAGCATCCTATGATCAGATT	CGTAACCCAGAATACCCTTGAGTTT
UBC1			CCGTTTGTAGAGCCATAATTGCA	AGGTTGCCTGAGTCACAGTTAAGTG
LOC_Os03g49400	28116620	28124217	TCTTTCCCGTACCCTTGGAC	TGCCGATACACATCGACAGA
LOC_Os03g49500	28169807	28173984	AGCCCTCAGGATCTACCTCA	AGATGTGCCCTCCCATCAAA
LOC_Os03g49620	28254419	28259880	CCAACGTCCTGCTTGATGAG	GCGCAATGTGACCCATAGTT
LOC_Os03g53150	30480660	30483331	GGTGAATGGCTCTGATGCTG	CCTCAAGCGTTTGCATGACT
LOC_Os03g56050	31921933	31925513	TTCCACGCACATCAACTTCC	CCTGCCTGCTCATGTTCTTC
LOC_Os03g57640	32851425	32852782	CAAACTGAGCTGCCTGAGTC	TAGTCCTCGAAGCGGATCAC
LOC_Os03g52450	30094292	30099092	AAAGGCCAGTTTGCTGGAAG	CCACAGGCATTACAGAGGGA
LOC_Os03g56060	31930541	31934624	CGTCGAGTGCCAATGTGAAT	GAGCTTCCGGAGAAGGAAGA
LOC_Os03g53880	30890100	30899911	TACAGACTTTGGCCTCAGCA	GTTCCAGCTCCCTGAGAAGT
LOC_Os03g55290	31465625	31464840	CCTCCTCTTCCCTCCAAGTT	TACTTGAGGCAGTCGTCGTG
LOC_Os03g58260	33193735	33198078	CAGGTGCACGCTCAAATGTA	CCGATGATCACACCATCTGC
LOC_Os03g58290	33207531	33210400	AAAGAAGCTGGTGTGCAAGG	TCATCCTCTCTCCCGGTGTA
LOC_Os03g58300	33217418	33214533	GGCATGCTCTTTCAGGAGTG	CCTTCATCCTGTCTGGTGGT
LOC_Os03g58320	33226460	33228543	GCTGGTGCTGCTTACTACAC	AAAGCCAACACACACAGCTT

样品编号	Changai	L-Pool	S-Pool	IR 145
Clean reads	160733360	189587718	223654650	145947156
Clean bases(bp)	24110004000	28438157700	33548197500	21892073400
Mapped reads	157946429	186412438	220135923	142034376
Mapped bases(bp)	23691964350	27762740240	32098485368	21305156400
Mapping rate	98.27%	98.33%	98.43%	97.32%
Duplicate reads	26216469	35168893	38980737	18236886
Duplicate rate	16.60%	18.87%	17.71%	12.84%
Mismatch bases(bp)	309119777	369422281	396469736	310450630
Mismatch rate	1.30%	1.33%	1.24%	1.46%
Average sequencing depth	51.32	57.83	66.53	47.49
Coverage	91.95%	95.90%	98.82%	92.53%
Coverage at least 4X	88.98%	93.47%	95.62%	89.25%
Coverage at least 10X	85.93%	90.72%	91.91%	86.24%
Coverage at least 20X	82.13%	86.27%	87.90%	82.48%
Coverage at least 50X	36.81%	46.49%	61.40%	15.04%

候选基因 Candidate gene	基因名称 Gene name	注释信息 Annotation
LOC_Os03g56050	OsAP23	AP2-like ethylene-responsive transcription factor Aintegumenta
LOC_Os03g57640	OsGID1L2	Gibberellin receptor GID1L2
LOC_Os03g52450	OsGATA19a	GATA transcription factor 25
LOC_Os03g56060	OsCSLC9	CSLC9 - cellulose synthase-like family C
LOC_Os03g58300	OsIGL1	indole-3-glycerol phosphate lyase, chloroplast precursor
LOC_Os03g58320	OsIGL2	indole-3-glycerol phosphate lyase, chloroplast precursor
LOC_Os03g58290	OsIGL3	indole-3-glycerol phosphate lyase, chloroplast precursor

位点/基因	标记区间	位置（bp）	LOD值	解释变异	群体	参考文献
QTL/Gene	Marker interval	Position	LOD value	R²（%）	Population	Reference
-	RZ403-RZ448	-	4.73	17.5	-	Redona et al., 1996
-	RZ403-RZ630	-	3.33	10.3	-	Redona et al., 1996
qml3	RZ403-RG179	-	3.67	11.32	DH	Cao et al., 2002
-	G232-R1927	-	3.11	-0.59	RILs	Cai et al., 2002
-	R1927-BCD450	-	5.51	0.67	RILs	Cai et al., 2002
-	BCD450-RZ393	-	3.04	-0.56	RILs	Cai et al., 2002
qml3-1	RZ517-RZ399	-	4.67	7.1	RILs	OUYANG et al., 2005
qml3-2	RZ328-RZ575	-	3.45	6	RILs	OUYANG et al., 2005
qml3-3	RZ696-RZ22	-	4.43	8.1	RILs	OUYANG et al., 2005
qLOE-3	RM3919-RM520	-	2.548	10.7	DH	Zhang et al., 2006
-	RM426-RM448	-	8.93	24.97	RILs	Huang et al., 2010
-	RM426-RM514	-	15.52	33.36	RILs	Huang et al., 2010
-	R3226/R1927/R1925	-	4.2	11.5	BILs	Lee et al., 2012b
-	C595/R1927/R1925	-	7.5	20.8	BILs	Lee et al., 2012b
-	RM8208-RM8277	-	2.8	6.5	-	Lee et al., 2012a
-	R1618	-	12.09	37.56	BILs	Lee et al., 2017
-	R1618	-	7.18	26.97	BILs	Lee et al., 2017
LOC_Os03g51340	-	29376077-29378021	-	-	-	Zhao et al., 2018
LOC_Os03g53320	-	30603235-30602885	-	-	-	Zhao et al., 2018
LOC_Os03g53340	-	30607159-30604067	-	-	-	Zhao et al., 2018
LOC_Os03g06070	-	3039736-3045376	-	-	-	Wu et al., 2015
LOC_Os03g06139	-	3085989-3075919	-	-	-	Wu et al., 2015
LOC_Os03g39790	-	22138216-22135801	-	-	-	Wu et al., 2015
LOC_Os03g40040	-	22244649-22243187	-	-	-	Wu et al., 2015
LOC_Os03g40084	-	22268809-22270021	-	-	-	Wu et al., 2015
LOC_Os03g40110	-	22292562-22285683	-	-	-	Wu et al., 2015
LOC_Os03g40194	-	22351524-22347660	-	-	-	Wu et al., 2015
LOC_Os03g40390	-	22440834-2248628	-	-	-	Wu et al., 2015

染色体	基因名称	基因登录号	位置（bp）	参考文献
Chromosome	Gene name	Gene accession	Position	Reference
1	OsGY1	LOC_Os01g67430	39177169-39178676	Xiong et al., 2017
5	OsGSK2	LOC_Os05g11730	6661493-6657481	Sun et al., 2018
8	OsSMAX1	LOC_Os08g15230	9228110-9224161	Zheng et al., 2020

Combining QTL-seq and linkage analysis to identify the QTL of mesocotyl elongation in rice (Oryza sativa L.)

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