Identification of stable quantitative trait loci for grain yield in rice

Silva, Daniany Rodrigues Adorno; Mendonça, João Antônio; Cordeiro, Antônio Carlos Centeno; Magalhães Júnior, Ariano Martins de; Vianello, Rosana Pereira; Brondani, Claudio

doi:10.1590/S1678-3921.pab2022.v57.02812

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Genetics, Original Article • Pesq. agropec. bras. 57 • 2022 • https://doi.org/10.1590/S1678-3921.pab2022.v57.02812 copy

Identification of stable quantitative trait loci for grain yield in rice

Identificação de locos quantitativos estáveis quanto à produtividade de grãos em arroz

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

The objective of this work was to identify the quantitative trait loci (QTLs) associated with grain yield in a rice segregant population (GYP). A population of 245 inbred recombinant rice lines from the 'Epagri 108' (Oryza sativa subsp. indica) x 'IRAT 122' (O. sativa subsp. japonica) cross was evaluated at different locations and years and genotyped by single nucletide polymorphism (SNP) markers. A map of 1,592.8 cM was obtained from 9,831 SNPs, identifying 25 QTLs. The following nine SNPs showed stability between the different environments: M1.37719614 and M6.9563117 for GYP; M4.29340056, M5.25588710, M7.29115624, and M12.4534450 for 100-grain weight (HGW); and M1.38398157, M4.28368337, and M7.25991230 for plant height (PH). Six SNPs were not present in the linkage blocks: M6.9563117 and M4.1077080 for GYP; M5.25588710 and M6.8886398 for HGW; and M2.34471005 and M8.5955948 for PH. The M6.9563117 and M5.25588710 SNPs were considered environmentally stable and were not present in the linkage blocks, showing their high potential for use in marker-assisted selection for grain yield in Brazilian rice breeding programs.

Index terms:
Oryza sativa ; DArTseq; genotyping by sequencing; heritability; molecular markers

Environment	Location – city, state	Year	Coordinates			GYP (kg ha⁻¹)	HGW (g)	PH (cm)
Environment	Location – city, state	Year	Latitude	Longitude	Altitude (m)	GYP (kg ha⁻¹)	HGW (g)	PH (cm)
GO/Y1	Goiânia, GO	2014	16°30’23’’S	49°17’00’’W	823	9,147.3–2,073.6	3.3–2.4	130.4–79.9
GO/Y2	Goiânia, GO	2016	16°30’23’’S	49°17’00’’W	823	8,096.3–3,321.8	-	177.4–99.3
GO/Y3	Goiânia, GO	2017	16°30’23’’S	49°17’00’’W	823	4,7901–1,089.8	-	132.3–91.0
RR	Boa Vista, RR	2014	2°45’26’’N	60°43’51’’W	83	8,958.1–3,185.0	-	125.8–84.0
RS	Pelotas, RS	2014	31°40’49’’S	52°26’23’’W	61	9,236.4–2,671.4	3.3–2.3	127.8–79.9

Component⁽¹⁾	Location⁽²⁾	GYP	HGW	PH
Component⁽¹⁾
F-value	GO/Y1	34.1***	198.2***	88.26***
	GO/Y2	4.4**	–	8.74***
	GO/Y3	3.8***	–	8.2***
	RR	60.5***	–	92.86***
	RS	33.9***	184.9***	86.8***
	ME	13.2**	–	19.3**
	MY	6.06*	–	61.18***
σ²_G	GO/Y1	2,996,945	0.047	400.8
	GO/Y2	1,144,844	–	188.19
	GO/Y3	695,880	–	195.48
	RR	2,346,000	–	223.3
	RS	2,275,011	0.039	157.2
	ME	2,480,000	–	150.8
	MY	965,300	–	1.38e-5
σ²_P	GO/Y1	3,354,160	0.055	423.9
	GO/Y2	4,841,642	–	327.8
	GO/Y3	901,627,5	–	249.49
	RR	2,607,450	–	236.4
	RS	3,154,293	0.053	205.8
	ME	3,176,300	–	360.01
	MY	1,459,496	–	23.85
CV (%)	GO/Y1	15.73	4.38	5.96
	GO/Y2	59.27	–	13.94
	GO/Y3	21.45	–	8.95
	RR	11.05	–	5.34
	RS	25.12	5.66	9.69
AC	GO/Y1	0.94	0.92	0.97
	GO/Y2	0.49	–	0.75
	GO/Y3	0.88	–	0.88
	RR	0.95	–	0.97
	RS	0.85	0.86	0.87
H²	GO/Y1	0.89	0.85	0.94
	GO/Y2	0.24	–	0.57
	GO/Y3	0.77	–	0.78
	RR	0.90	–	0.94
	RS	0.72	0.74	0.76

Chromosome	Total SNP markers	Total filtered SNP markers	Total distance (Mbp)	Total distance (cM)	Average distance between SNPs (cM)	Average Density of SNPs (kbp/SNP)
1	1,962	1,875	43	203.86	0.11	23
2	1,493	1,432	36	175.13	0.12	25
3	833	730	36	194.58	0.27	50
4	1,061	538	35	130.59	0.24	65
5	1,209	966	28	120.41	0.12	29
6	920	397	27	114.08	0.29	69
7	639	590	29	155.62	0.26	49
8	617	571	28	117.31	0.21	49
9	731	316	23	92.38	0.29	72
10	565	506	23	92.99	0.18	46
11	990	822	29	94.26	0.11	35
12	1,263	1,088	27	100.87	0.09	25
Total	12,283	9,831	364	1,592.08	0.19*	44.8*

Trait⁽¹⁾	QTL	LD interval⁽²⁾ (bp)	Gene number	SNP marker	GO/Y1⁽³⁾				RR				RS				ME
Trait⁽¹⁾	QTL	LD interval⁽²⁾ (bp)	Gene number	SNP marker	LOD	Pos	Add	R²	LOD	Pos	Add	R²	LOD	Pos	Add	R²	LOD	Pos	Add	R²
GYP	qGYP1.1	20608740..21083225	66	M1.20784324	5	77.8	-303.2	5	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP1.2	37362221..37925006	93	M1.37719614	14	165.8	-489.4	13	-	-	-	-	-	-	-	-	4	164.2	36	7
	qGYP3.1	3447267.3447286	–	M3.3447267	6	25	-297.6	5	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP3.2	35670223..36412933	125	M3.35771748	4	189.1	265.4	3	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP4	–	-	M4.1077080	5	8	270.8	4	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP6	-	-	M6.9563117	24	47	-722.2	25	-	-	-	-	-	-	-	-	6	52.6	-44	9
	qGYP9.1	15703948..15951147	29	M9.15873858	-	-	-	-	-	-	-	-	3	51	-451.6	7	-	-	-	-
	qGYP10	17304937.. 17318753	2	M10.17304937	-	-	-	-	3	53.2	-307.1	6	-	-	-	-	-	-	-	-
	qGYP11	4937420..5439040	84	M1l.5245849	3	31.4	-223.8	3	-	-	-	-	-	-	-	-	-	-	-	-
	TOTAL				44			56	10			19	3			7	10			18
HGW	qHGW1	1724593..2297175	90	M1.2078044	3	12.2	0.03	4	-	-	-	-	-	-	-	-	-	-	-	-
	qHGW4	28680378..29442097	92	M4.29340056	-	-	-	-	-	-	-	-	-	-	-	-	5	98.1	0.005	7
	qHGW5	–	-	M5.25588710	7	101.1	-0.05	9	-	-	-	-	-	-	-	-	4	107.7	0.005	7
	qHGW6	–	-	M6.8886398	3	49	-0.03	4	-	-	-	-	-	-	-	-	-	-	-	-
	qHGW1	28858818..29586014	109	M7.29115624	-	-	-	-	-	-	-	-	-	-	-	-	3	153.3	0.005	5
	qHGW10	17440110..17905986	55	M10.17759332	4	55.8	-0.03	5	-	-	-	-	-	-	-	-	-	-	-	-
	qHGW12.1	4254605..4668537	55	M12.4534450	5	31.6	0.04	7	-	-	-	-	3	32	-0.05	8	-	-	-	-
	qHGW12.2	25842248..26273116	56	M12.25886429	4	92.8	0.03	4	-	-	-	-	-	-	-	-	-	-	-	-
	TOTAL				24			36					3			8	11			19
PH	qPH1	38000079..38689259	111	M1.38398157	66	168	-9.1	69	10	170	-3.2	18	10	159	4.96	23	53	168	-7	62
	qPH4	27916117..28661996	103	M4.28368337	3	97	-1.4	2	-	-	-	-	-	-	-	-	4	93	1	2
	qPH7	25660807..26268775	104	M7.25991230	6	153	-1.7	3	-	-	-	-	-	-	-	-	-	-	-	-
	qPH8	–	2	M8.5955948	-	-	-	-	3	42	-1.8	6	-	-	-	-	-	-	-	-
	TOTAL				68			72	13			24	10			23	53			63

Trait⁽¹⁾	QTL	LD interval⁽²⁾ (bp)	Gene number	SNP marker	Y1 (2014)				Y2 (2016)				Y3 (2017)				MY⁽³⁾
Trait⁽¹⁾	QTL	LD interval⁽²⁾ (bp)	Gene number	SNP marker	LOD	Pos	Add	R²	LOD	Pos	Add	R²	LOD	Pos	Add	R²	LOD	Pos	Add	R²
GYP	qGYP1.1	20608740..21083225	66	Ml.20784324	5	77.8	-303.2	5	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP1.2	37362221..37925006	93	Ml.37719614	14	165.8	-489.4	13	-	-	-	-	-	-	-	-	5	165.8	-173.1	13
	qGYP2	23548832..2528326	258	M2.23548832	-	-	-	-	2	108.2	147.4	7	-	-	-	-	-	-	-	-
	qGYP3.1	3447267.3447286	-	M3.3447267	6	25	-297.6	5	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP3.2	35670223..36412933	125	M3.35771748	4	189.1	265.4	3	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP4	–	-	M4.1077080	5	8	270.8	4	-	-	-	-	-	-	-	-	-	-	-	-
	qGYP6	–	-	M6.9563117	24	47	-722.2	25	-	-	-	-	8	52.6	-353.7	20	9	47	-239.9	22
	qGYP9.2	21782549..22925474	210	M9.22544728	-	-	-	-	-	-	-	-	3	91.8	-217.9	9	-	-	-	-
	qGYP11	4937420..5439040	84	Mil.5245849	3	31.4	-223.8	3	-	-	-	-	-	-	-	-	-	-	-	-
	TOTAL				44			56	2			7	10			30	14			38
PH	qPH1	38000079..38689259	111	Ml.38398054	66	168	-9.1	69	18	167.8	-7.7	46	46	167.8	-10.6	77	48	167.8	-13.7	80
	qPH2	–	-	M2.34471005	-	-	-	-	-	-	-	-	4	167.7	-1.8	3	-	-	-	-
	qPH3	33433409..33550772	20	M3.33466106	-	-	-	-	-	-	-	-	3	175.8	1.5	2	-	-	-	-
	qPH4	27916117..28661996	103	M4.28368337	3	97	-1.4	2	-	-	-	-	-	-	-	-	-	-	-	-
	qPH7	25660807..26268775	104	M7.25991230	6	153	-1.8	3	-	-	-	-	-	-	-	-	3	133.3	-1.5	2
	Total				68			72	18			46	46			79	49			81

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