Assessment of SNP and InDel Variations Among Rice Lines of Tulaipanji x Ranjit

doi:10.1016/j.rsci.2017.01.003

Abstract

Abstract:

Genotyping by sequencing (GBS) is the recent approach of next-generation sequencing technique for discovering and genotyping single nucleotide polymorphisms (SNPs) in crop species. Genotypic variation studies (SNPs and insertion-deletions/InDels) were performed using four rice lines based on GBS data by aligning to the reference genome Nipponbare. Local aromatic rice landrace Tulaipanji was crossed with Ranjit, and two distinct lines were identified from the progenies: one line with awns and aroma traits and the other without awns and aroma. Total number of SNPs and InDels identified were 52 810 and 4 327 at read depth 10, respectively. Out of the total polymorphic SNPs/InDels, 16 490 were intergeneric, 7 812 were inside gene, and 4 435 were intronic. Phylogenetically, Tulaipanji was closer to the reference genome nipponbare. Based on recurrent parent genome analysis, out of 10 013 alleles, 92.52% was introgressed into progeny-awn from Tulaipanji and 7.48% from Ranjit, whereas progeny-awnless carried 89.19% alleles from Ranjit and only 10.81% alleles from Tulaipanji. In addition, progeny-awn was the highest heterozygous (83.88%) and progeny-awnless was the least (2.24%) at this fifth generation of recombinant inbred lines. These SNP variations may be linked to the phenotypic traits and can be utilized in crop improvement through linkage mapping. These results suggest that adding a high density of SNP markers to a mapping or breeding population through GBS has a great value for numerous applications in rice breeding and genetics research.

Key words: rice, genotyping by sequencing, insertion-deletion, genomic introgression, single nucleotide polymorphism, awn, aroma, heterozygous

Chandra Roy Subhas, Bhasker Reddy Lachagari Vijaya. Assessment of SNP and InDel Variations Among Rice Lines of Tulaipanji x Ranjit[J]. Rice Science, 2017, 24(6): 336-348.

Figures/Tables 11

References 98

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Sample	Grain length (mm)	Grain width (mm)	1000-grain weight (g)	Awn length (mm)
Tulaipanji	7.73	1.88	15.72	21.01
Ranjit	8.07	2.39	18.62	0
Progeny-awn	7.85	1.98	15.45	14.77
Progeny-awnless	8.46	2.25	17.52	0

Sample	Grain length (mm)	Grain width (mm)	1000-grain weight (g)	Awn length (mm)
Tulaipanji	7.73	1.88	15.72	21.01
Ranjit	8.07	2.39	18.62	0
Progeny-awn	7.85	1.98	15.45	14.77
Progeny-awnless	8.46	2.25	17.52	0

Sample	Number of raw reads (bp)	Number of bases (bp)		GC content (%)		Percentage of data (%)		Raw read length	Number of preprocessed reads (bp)
Tulaipanji	4 108 370	410 830 000		40.7		92.24		100×2	4 055 808
Ranjit	2 890 990	289 090 000		41.2		92.21		100×2	2 835 872
Progeny-awn	3 099 014	309 900 000		42.8		91.66		100×2	3 046 924
Progeny-awnless	3 131 956	313 190 000		43.1		91.91		100×2	3 091 894
Sample	Percentage of preprocessed reads (%)		Number of reads aligned (bp)		Percentage of reads aligned (%)		Number of uniquely aligned reads (bp)		Percentage of uniquely aligned reads (%)
Tulaipanji	98.72		3 564 468		87.89		3 450 006		96.78
Ranjit	98.09		2 417 235		85.24		2 326 571		96.24
Progeny-awn	98.31		2 681 183		88.00		2 596 873		96.85
Progeny-awnless	98.72		2 697 221		87.24		2 587 535		95.93

Sample	Number of raw reads (bp)	Number of bases (bp)		GC content (%)		Percentage of data (%)		Raw read length	Number of preprocessed reads (bp)
Tulaipanji	4 108 370	410 830 000		40.7		92.24		100×2	4 055 808
Ranjit	2 890 990	289 090 000		41.2		92.21		100×2	2 835 872
Progeny-awn	3 099 014	309 900 000		42.8		91.66		100×2	3 046 924
Progeny-awnless	3 131 956	313 190 000		43.1		91.91		100×2	3 091 894
Sample	Percentage of preprocessed reads (%)		Number of reads aligned (bp)		Percentage of reads aligned (%)		Number of uniquely aligned reads (bp)		Percentage of uniquely aligned reads (%)
Tulaipanji	98.72		3 564 468		87.89		3 450 006		96.78
Ranjit	98.09		2 417 235		85.24		2 326 571		96.24
Progeny-awn	98.31		2 681 183		88.00		2 596 873		96.85
Progeny-awnless	98.72		2 697 221		87.24		2 587 535		95.93

Sample	At read depth 2			At read depth 5			At read depth 10
Sample	No. of SNPs	No. of InDels	Total	No. of SNPs	No. of InDels	Total	No. of SNPs	No. of InDels	Total
Tulaipanji	12 972	925	13 897	10 218	701	10 919	7 476	489	7 965
Ranjit	18 042	1 703	19 745	13 510	1 300	14 810	9 966	950	10 916
Progeny-awn	31 303	2 383	33 686	25 760	1 988	27 748	19 559	1 514	21 073
Progeny-awnless	26 097	2 262	28 359	21 028	862	22 890	15 809	1 374	17 183