鹰嘴豆（Cicer arietinum L.）开花时间、脱壳率、收获指数及相关性状的全基因组关联研究

IF 1.6 3区农林科学 Q2 AGRONOMY

Euphytica Pub Date : 2024-08-22 DOI:10.1007/s10681-024-03398-z

N. Shivanagouda Patil, Venkatraman Hegde, K. K. Vinod, Swarup K. Parida, Pradeep Kumar Jain

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引用次数: 0

摘要

谷物产量是生物量（BM）和收获指数（HI）的乘积。在印度北部平原的长季节环境中，HI 而非 BM 是制约鹰嘴豆产量的主要因素。这是首次利用基因分型测序方法对鹰嘴豆的脱壳率（Sh.%）、HI 及相关性状进行全基因组关联研究（GWAS）。对涉及品种、特定性状基因型和先进育种品系的 178 个种质系进行基因分型，发现了 35,795 个高通量单核苷酸多态性（SNPs）。研究的目的是揭示造成鹰嘴豆开花时间、脱壳率、HI 和相关性状变异的基因组区域。对三种环境的表型分析表明，HI 和相关性状之间存在较高的变异性和关联性。种群结构分析显示有两个亚种群（k = 2）。连锁不平衡（LD）广泛，LD衰减相对较低。利用 FarmCPU 模型共鉴定出 172 个 HI 及相关性状的标记-性状关联（MTAs），其中 50%开花天数（DAF）、HI 和脱壳率表现出显著关联。目前的研究为生物量、荚果和种子产量/株、荚果和种子数/株 HI 和脱壳率分别确定了一致的多效性 MTA，即 SNC_021165.1_57891716 和 SNC_021165.1_57917493、SNC_021164.1_6073633 和 SNC_021165.1_33405826。在 SYPL 和 PYPL 中观察到的所有 MTAs 以及在 HI 和 BM 中观察到的最大数量的 MTAs 都位于同一条 6 号染色体上。此外，PPL 和 SN 的最多 MTA 分布在 5 号染色体上。其中一个重要发现是，SYPL、PYPL、BM 和 100SW 的大多数 MTAs 都分布在第 6 号染色体的 25 kb 基因组区域内。共有 16 个 MTAs 被保留用于 Insilco 分析（- log10(p) > 4.0），并在 100 kb 的侧翼区域与参考基因组进行了候选基因搜索。DAF的候选基因数量最多（50），其次是Sh.%（48）、HI（16）、SYPL（13）、BM（10）和PYPL（8）。DAF、Arabinogalactan 蛋白和五胜肽重复的转录本参与了拟南芥的开花过程。就PYPL和SYPL而言，MTA与编码五肽重复、丝氨酸/苏氨酸蛋白激酶和E3泛素蛋白连接酶的基因有关。这些转录本主要在花粉成熟、受精和开花时间方面发挥作用。与 HI 相关的伴侣蛋白 DnaJ 和 Sh.% 的受体样蛋白激酶（RLK）分别参与了拟南芥和水稻产量的提高。本研究还验证了与 DAF 相关的一个 MTA，其 r2 值为 12.62%。

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Genome wide association studies for flowering time, shelling percentage, harvest index and related traits in chickpea (Cicer arietinum L.)

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Genome wide association studies for flowering time, shelling percentage, harvest index and related traits in chickpea (Cicer arietinum L.)

Grain yield is a product of biomass (BM) and harvest index (HI). HI, not BM, is the major constraint of chickpea productivity in the long season environments of northern Indian plains. This is the first genome wide association study (GWAS) of shelling percentage (Sh.%), HI and related traits in chickpea using genotyping by sequencing approach. Genotyping of 178 germplasm lines involving varieties, trait specific genotypes and advance breeding lines found 35,795 high-throughput single nucleotide polymorphisms (SNPs). The objectives of the study were to unravelling the genomic regions responsible for variation in flowering time, shelling percentage, HI and related traits in chickpea. The phenotypic analysis across three environments showed high variability and connections among HI and related traits. Population structure analysis revealed two sub-populations (k = 2). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 172 marker-trait associations (MTAs) were identified for HI and related traits using FarmCPU model, of which days to 50% flowering (DAF), HI and shelling percentage showed significant associations. The current study has identified consistent pleiotropic MTAs, SNC_021165.1_57891716 and SNC_021165.1_57917493, SNC_021164.1_6073633 and SNC_021165.1_33405826 for biomass, pod and seed yield/plant, pod and seed number/plant HI and Sh.%, respectively. All the MTAs observed for SYPL, PYPL and maximum number of MTAs for HI and BM were located on the same chromosome number 6. Further maximum number of MTAs for PPL and SN were distributed on chromosome 5. One of the important findings is that most of the MTAs for SYPL, PYPL, BM, and 100SW are distributed within 25 kb genomic region of chromosome 6. A total of 16 MTAs were retained for Insilco analysis (− log10(p) > 4.0) and searched for their candidate genes in a 100-kb flanking region against the reference genome. The maximum number of genes noticed for DAF (50), followed by Sh.% (48), HI (16), SYPL (13), BM (10), and PYPL (8). The transcripts for DAF, Arabinogalactan proteins and pentatricopeptide repeat were involved in flowering of Arabidopsis. For both PYPL and SYPL, MTA found linked to the genes coding for pentatricopeptide repeat, serine/threonine-protein kinase and E3 ubiquitin-protein ligase. These transcripts played role mainly in pollen maturation, fertilization and flowering time. Chaperone protein DnaJ linked to HI, and receptor-like protein kinase (RLK) for Sh.% were involved in improving yield in Arabidopsis and rice, respectively. The present study also validated one of the MTA linked to DAF which showed r² value of 12.62%.

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来源期刊

Euphytica 农林科学-农艺学

CiteScore

3.80

自引率

5.30%

发文量

157

审稿时长

4.5 months

期刊介绍： Euphytica is an international journal on theoretical and applied aspects of plant breeding. It publishes critical reviews and papers on the results of original research related to plant breeding. The integration of modern and traditional plant breeding is a growing field of research using transgenic crop plants and/or marker assisted breeding in combination with traditional breeding tools. The content should cover the interests of researchers directly or indirectly involved in plant breeding, at universities, breeding institutes, seed industries, plant biotech companies and industries using plant raw materials, and promote stability, adaptability and sustainability in agriculture and agro-industries.