Table 2.

RNA3–sgRNA3a recombination from in vitro reactions and from C. quinoa inoculations: summary of restriction analysis of the RT-PCR products.

Experiment
In vitro (RdRp reaction)a	Total number of cDNA clones analyzed	Number of recombination			Recombinants frequency (%)
1. RW(−) RNA3 + JS-21 sgRNA3a	60	5			8
2. RW(−) RNA3 + JS-14 sgRNA3a	60	0			0
3. RW(−) RNA3 + JS-0 sgRNA3a	60	0			0
In whole plants (C. quinoa)b	Total number of cDNA clones analyzed	Distribution of restriction sitesc			Recombination frequency (%)
1. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a (0.2×)	No infection	No infection			No infection
2. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a (0.5×)	No infection	No infection			No infection
		BamHI/PstI	PstI	BamHI
3. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a (1.5×)	22	20	0	1	100
4. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a (3.0×)	21	21	0	0	100
5. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a (5.0×)	35	32	1	2	100
6. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-0 sgRNA3a (1.5×)	No infection	No infection			No infection
7. Wt RNAs 1 and 2 + B3-33del RNA3 + JS-0 sgRNA3a (5.0×)	No infection	No infection			No infection
8. Wt RNAs 1 and 2 + B3-33del RNA3	No infection	No infection			No infection

^aSee Materials and methods for the in vitro recombination assays.

^bThe co-inoculation with wt RNAs 1 and 2 + B3-33del RNA3 + JS-21 sgRNA3a generated, on average, from one to three local lesions per each inoculated leaf (three leaves of two C. quinoa plants) from two independent experiments. The lesion tissue was cut out, combined, and the virus extracted, followed by cDNA cloning of viral RNA, and analysis of cDNA clones by sequencing (see also Materials and methods and Fig. 8). The numbers in parentheses: 0.2×, 0.5×, 1.5×, 3.0× and 5.0× indicate the molar ratio of sgRNA3a to RNA3 in the used RNA inoculation mixtures.

^cThe numbers show the amount of cDNA clones carrying the restriction markers as listed.